WISARD[wɪzərd]
Workbench for Integrated Superfast Association study with Related Data
HOME  |   DOWNLOAD  |   OPTIONS  |   TROUBLE?  |   LOGIN
 
optname shortname haveexclrequ havetype havedetail
--quiet-qOOO
--version-vOOO
--ped-iOOO
--lgen-lOOO
--bed-jOOO
--tped-tpOOO
--fam-FOOO
--out-oOOO
--data-DXXX
--verbose-vbOOO
--thread-tOOO
--kinship-kOOO
--sampvar-hOOO
--sampvarflag-aiXXX
--variantvar-aOOO
--filvariant-fkOOO
--incvariant-ikOOO
--filgeno-fjOOO
--incgeno-ijOOO
--pname-nOOO
--corpair-caOOO
--corgrm-cgOOO
--corepacts-epXXX
--remsamp-irOOO
--selsamp-isOOO
--nasamp-xsOOO
--randnasamp-rxOOO
--remvariant-srOOO
--selvariant-SsOOO
--remfam-fFOOO
--selfam-iFOOO
--filrange-rrOOO
--incrange-rsOOO
--varresize-szOOO
--varwindow-vwXXX
--sampresize-azOOO
--emcount-ecOOO
--aithr-atOOO
--autoonly-UOOO
--sexonly-sxOOO
--chr-chOOO
--freq-fOOO
--hwe-HOOO
--makeblup-muOOO
--filmaf-ffXXX
--filmac-fmOOO
--filhwe-fhOOO
--filgind-fgOOO
--filgvar-fpOOO
--filnf-fNOOO
--filmf-fsOOO
--filcase-faOOO
--filcontrol-ftOOO
--filmispheno-foOOO
--filsample-fnOOO
--filgdist-fiOOO
--filnosex-fxOOO
--filmale-flOOO
--filfemale-feOOO
--snvonly-voOOO
--indelonly-xoOOO
--incmaf-ifXXX
--incmac-imOOO
--inchwe-ihOOO
--incgind-igOOO
--incgvar-ivOOO
--incgdist-iiOOO
--incsample-inOOO
--set-sOOO
--scoretest-ctOOO
--heritability-heOOO
--ml-mlOOO
--blup-bOOO
--prevalence-pvOOO
--medcor-McOOO
--imputepheno-ipOOO
--cname-cnOOO
--cor-cOOO
--makecor-MCOOO
--cordiag1-cdOOO
--empiall-eaOOO
--corpearson-cpOOO
--indep-idOOO
--mispheno-mhOOO
--misgeno-mgOOO
--1case-x1OOO
--cact-ccOOO
--1sex-s1OXO
--mafe-MFOOO
--ginv-giOOO
--makecov-mcOOO
--makepheno-mPOOO
--makeflag-MfXXX
--bim-biOOO
--founderonly-FoOOO
--famsummary-FsOOO
--ncsummary-ncOOO
--ibs-bsOOO
--seed-SOOO
--map-MOOO
--specdcmp-sdOOO
--runas-rOOO
--nostop-xxOOO
--x-xOOO
--x2-x2OOO
--ignoreparent-IpOOO
--ignorefid-IfOOO
--nofid-NfOOO
--sepid-SiXXX
--noparent-npOOO
--nosex-nXOOO
--nopheno-nPOOO
--nopos-noOOO
--nogdist-ngOOO
--probandcol-pbOOO
--twincol-twOOO
--noweight-ewOOO
--betaweight-bwOOO
--mafweight-MwOOO
--hybrid-hyOOO
--gsmacthr-gtOOO
--chrwise-cwOOO
--est-EOOO
--weight-wOOO
--nomap-nmOOO
--makeclgeno-mzOOO
--indel-IDOOO
--logistic-lgOOO
--sortvariant-svOOO
--sortpos-spOOO
--sortsample-ssOOO
--sortiid-siOOO
--baseline-blOOO
--gz-ZOOO
--ktau-ktOOO
--empktau-ekOOO
--makenrm-myOOO
--makeweight-mwOOO
--nosampvarhdr-nhOOO
--pvalrange-prOOO
--time-tiOOO
--phenostdize-pzOOO
--outmispheno-opOOO
--outmisgeno-ogXXX
--gxecovs-gcOOO
--passemptyline-peOOO
--listvariant-lmOOO
--listsample-lsOOO
--listfounder-lfOOO
--nolmm-nlOOO
--geneset-pwOOO
--gsetconsec-GCXXX
--nosysfeat-nsOOO
--fname-fcOOO
--makeev-mVOOO
--ev-evOOO
--natural-ntOOO
--dupnaming-dpOOO
--acgt-acOOO
--1234-zzOOO
--sepallele-saOOO
--consecallele-clOOO
--citation-ceOOO
--miss-mxOOO
--misparent-mqOOO
--sampmajor-smOOO
--nospecdcmp-neOOO
--species-scXOO
--nodata-ndXOO
--regex-erXXX
--model-JXXX
--fqls-qfOOO
--fqlsnopddt-pfOOO
--retestthr-rtOOO
--mqls-qmOOO
--mfqls-qxOOO
--avail-avOOO
--heri-hiOOO
--mqlsconsec-qpOOO
--fastmqls-FaXXX
--fastfqls-FFXXX
--genetest-tgOOO
--genesummary-sgOOO
--gmapsummary-xgOOO
--pedcmc-pcOOO
--raremaf-rmOOO
--genemiss-gmOOO
--genesize-grOOO
--skato-soOOO
--skat-skOOO
--skatondiv-ovOOO
--skatodivs-ozOOO
--wsum-wsOOO
--kbac-KOXO
--kbacalpha-kaOXO
--kbac2side-k2OXO
--kbackernel-kkOOO
--mfhom-moOOO
--mfhet-mfOOO
--asum-auOOO
--makegeno-mZOOO
--farvat-FvOOO
--pedgene-pgXXX
--adjf1-f1XXX
--adjf2-f2XXX
--makefarvat-kfXXX
--farvatx-FxXXX
--farvatxndiv-XvXXX
--farvatxd-FdXXX
--qtest-QOOO
--qtestclump-QcOOO
--qteststt-QsOOO
--qtestbetacov-QbOOO
--makebeta-aaOOO
--mdr-mdOOO
--order-OOOO
--top-TOOO
--hmdr-hmOOO
--hmdrall-haXXX
--hmdrprior-hpXXX
--pharaoh-gsXXX
--proopt-hoXXX
--prolambda-PlXXX
--prorange-PrXXX
--prothr-PtXXX
--promaxiter-gqXXX
--progenesize-PgXXX
--progsetsize-ptXXX
--prosingle-PeXXX
--propermcov-PpXXX
--nperm-NeOOO
--seqperm-SPXXX
--permfile-PFXXX
--cv-cvOOO
--gesca-geXXX
--modeltype-MTXXX
--ggpath-gpXXX
--makecolgeno-mOXXX
--debug-dbXXX
--help-hlXXX
--dosage-dOOO
--expression-EXXXX
--vcf-VOOO
--simtrio-xtOOO
--nsim-sfXXX
--szvar-zOOO
--sim-sFXXX
--trio-sTOOO
--extfam-sEOOO
--nsig-nxOOO
--sigmaf-XMXXX
--simfreq-sqOOO
--mafvar-msOOO
--pca-POOO
--npc-NOOO
--proppc-ppOOO
--usemf-uOOO
--fullpca-fuOOO
--rpath-rlOOO
--grm-gROOO
--grmalpha-gaOOO
--makeped-mpOOO
--maketped-mTOOO
--makebed-mbOOO
--makeraw-mrOOO
--makedom-mDOOO
--makerec-mROOO
--makevcf-mvOOO
--makebcf-mFXOO
--makelgen-mnOOO
--makegen-mGOOO
--makebgen-mBOOO
--makebeagle-mLOOO
--makemdr-mMXXO
--zipbgen-zbOOO
--filqual-fqOOO
--incqual-iqOOO
--mendel-mOOO
--filmendelfam-rFOOO
--incmendelfam-xFOOO
--filmendelsamp-rSOOO
--incmendelsamp-xSOOO
--filmendelvar-dsOOO
--incmendelvar-xmOOO
--lrt-lrOOO
--vcfqc-vqOOO
--phasedonly-poOOO
--unphasedonly-uoOOO
--interactive-IOOO
--qls-qlOOO
--regression-rgOOO
--check-ckOOO
--gxe-gxOOO
--beta-beOOO
--rho-rhOOO
--rhopheno-rpOOO
--nsamp-NsOOO
--npheno-NpOOO
--noshuffle-NhOOO
--shuffle-shXXX
--powercalc-plOOO
--powercalc2-pxOOO
--split-slOOO
--merge-meOOO
--mergemode-mmOOO
--testmatrix-XmOOO
--testmatfunc-XtOOO
--testmatclass-XcOOO
--testfunc-XfOOO
--longitudinal-LOOO
--vt-vtOXO
--famvt-fvOOO
--ld-ldOOO
--ldcor-lcOOO
--annogene-agOOO
--annorange-arOOO
--annovar-asOXX
--gemma-GOOO
--density-deOOO
--tstv-ttOOO
--sep-xpOOO
--dsgdist-ddOOO
--pc2cov-p2OOO
--donull-dnOOO
--explore-eOOO
--updvariant-umOOO
--updchr-ucOOO
--updname-unOOO
--updgdist-udOOO
--updpos-upOOO
--updgeno-ugOOO
--ref-rfOOO
--tdt-tdOOO
--sdt-stOOO
--ldbin-lbOOO
--ldsize-lSOOO
--ldvar-lMOOO
--remna-rnOOO
--boost-boOOO
--thrboost-BtOOO
--quickepi-qeOOO
--ext-XOOO
--gmdr-gdOOO
--impute-ieOOO
--lod-loOOX
--makeimpute-miOOO
--sxa-xaOOO
--R-ROOO
--randbinpheno-rbOOO
--randpheno-reOOO
--genoctrl-glOOO
--usergc-egOOO
--adjust-AOOO
--famuniq-fUOOO
--popuniq-pUXOO
--monotone-tmOOO
--singleton-tsOOO
--doubleton-tbOOO
--genemdr-GmOOO
--variant2cov-m2OOO
--inbreed-ibOOO
--group-gOOO
--filgenic-fGOOO
--filintergenic-fIOOO
--variantsummary-ksOOO
--sampleorder-sOOOO
--variantorder-sMOOO
--cosi-coOOO
--setconsec-xcOOO
--setoverlap-xvOXX
--setrandom-xrXXX
--makeset-mSOOO
--settype-etOOO
--outcact-ocOOO
--out1case-o1OOO
--mistest-mtOOO
--incmistest-iMOOO
--filmistest-fMOOO
--nageno-NgOOO
--napheno-NHXXX
--filtreport-frOOO
--ggemma-zgOOO
--fisher-fyOOO
--trend-CAOOO
--genofield-gfOOO
--outphenoonly-ooOOO
--outnoheader-onOOO
--makemerlin-omOOO
--emmax-exXOX
--mds-MDXOX
--gxg-ggXOO
--invnorm-vnOOO
--fst-FtOOO
--forceconv-fVXXX
--out1234-t1OOO
--outacgt-oaOOO
--genesplit-GSOOO
--dfam-daXXO
--updallele-uaXOX
--window-WOOX
--ci-ciXOX
--lasso-laXOO
--lassolambda-llXOX
--lassoall-lLXOO
--pls-psXXX
--sampleweight-swXOX
--rvtdt-rdXOO
--fbskat-fKXOO
--nskip-nkXOO
--singleparent-sPXXX
--bcf-BOOX
--loocv-lvOOO
--mdrthr-dtOOX
--ldcontrast-lxXXX
--flip-fLXXX
--varsubset-fTXXX
--hethom-hhOXX
--markercheck-mkXXX
--meta-pXXX
--fid-xfXXX
--outformat-ofXXX
--maf-maXOX
--het-htXXX
--variantblup-vpXXX
--famsplit-FSXXX
--setspan-snXXX
--tridge-trXXX
--hamming-hnXXX
--baldingnichols-bnXXX
--fuzzymdr-zmXXX
--gxgall-gXXXX
--gxglist-xlXXX
--gxglambda-xbXXX
--prunevif-rvXXX
--prunepw-rwXXX
--selgene-gnXXX
--remgene-enXXX
OXX
OOO
OOO
OOO
OOO
OOO
OOO
OOO
OOO
OOO
OOO
OOO
OOO
XXO
Array ( [quiet] => Array ( [is_given_default] => false [is_essential] => false [longName] => --quiet [longAname] => [shortAname] => [shortName] => -q [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Suppress all visible outputs of execution. Note that the log will be normally produced. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Suppress all visible outputs of execution. Note that the log will be normally produced. ) [version] => Array ( [is_given_default] => false [is_essential] => false [longName] => --version [longAname] => [shortAname] => [shortName] => -v [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Print the version of WISARD and silently stop. No further analyses will be performed when this option is given. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Print the version of WISARD and silently stop. No further analyses will be performed when this option is given. ) [ped] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ped [longAname] => [shortAname] => [shortName] => -i [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Assigns input with one of PED/RAW format, full path of PED file with extension required [optExcl] => --vcf,--bcf,--bed,--tped,--dosage,--simtrio,--lgen,--simfam [optRequ] => * [optWith] => --map,--nomap,--indel,--acgt,--1234,--sepallele,--consecallele,--nskip [detaildesc] => Assigns input with one of PED/RAW format, full path of PED file with extension required ) [lgen] => Array ( [is_given_default] => false [is_essential] => false [longName] => --lgen [longAname] => [shortAname] => [shortName] => -l [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Assigns input with long format, full path of LGEN file with extension required [optExcl] => --ped,--vcf,--bcf,--bed,--tped,--dosage,--simtrio,--simfam [optRequ] => * [optWith] => --map,--fam,--indel,--acgt,--1234,--sepallele,--consecallele,--nskip [detaildesc] => Assigns input with long format, full path of LGEN file with extension required ) [bed] => Array ( [is_given_default] => false [is_essential] => false [longName] => --bed [longAname] => [shortAname] => [shortName] => -j [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Assigns input with PLINK Binary PED format. It is recommended to give full path with extension(.bed), but the extension can be omitted if an extension is <i>bed</i>. [optExcl] => --vcf,--bcf,--ped,--tped,--dosage,--simtrio,--lgen,--simfam [optRequ] => * [optWith] => [detaildesc] => Assigns input with PLINK Binary PED format. It is recommended to give full path with extension(.bed), but the extension can be omitted if an extension is <i>bed</i>. ) [tped] => Array ( [is_given_default] => false [is_essential] => false [longName] => --tped [longAname] => [shortAname] => [shortName] => -tp [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Assigns input with transposed PED format, full path of TPED file is required [optExcl] => --vcf,--bcf,--ped,--dosage,--bed,--simtrio,--lgen,--simfam [optRequ] => * [optWith] => [detaildesc] => Assigns input with transposed PED format, full path of TPED file is required ) [fam] => Array ( [is_given_default] => false [is_essential] => false [longName] => --fam [longAname] => [shortAname] => [shortName] => -F [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Use assigned path to load fam file when BED file has assigned as an input [optExcl] => * [optRequ] => * [optWith] => --bed/--tped/--lgen/--simfam/--vcf [detaildesc] => Use assigned path to load fam file when BED file has assigned as an input ) [out] => Array ( [is_given_default] => true [is_essential] => false [longName] => --out [longAname] => [shortAname] => [shortName] => -o [defVal] => res [optType] => file path [optCat] => RT_OTHER [desc] => Assigns output prefix, all outputs from WISARD will be generated with this prefix. [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Assigns output prefix, all outputs from WISARD will be generated with this prefix. ) [data] => Array ( [is_given_default] => false [is_essential] => false [longName] => --data [longAname] => [shortAname] => [shortName] => -D [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Shared data path ) [verbose] => Array ( [is_given_default] => true [is_essential] => false [longName] => --verbose [longAname] => [shortAname] => [shortName] => -vb [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Produce more detailed output and verbose log [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Produce more detailed output and verbose log ) [thread] => Array ( [is_given_default] => true [is_essential] => false [longName] => --thread [longAname] => [shortAname] => [shortName] => -t [defVal] => 1 [optType] => positive integer [optCat] => RT_POS [desc] => Set the number of threads will be used in the analysis, the number exceeds the thread count available on the system will be adjusted to maximum number of threads. [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Set the number of threads will be used in the analysis, the number exceeds the thread count available on the system will be adjusted to maximum number of threads. ) [kinship] => Array ( [is_given_default] => false [is_essential] => false [longName] => --kinship [longAname] => [shortAname] => [shortName] => -k [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Compute PDDT score matrix and substitute it as the sample correlation structure [optExcl] => --hybrid,--cor,--ibs,--corpearson,--indep,--ktau,--empktau,--empiall,--medcor [optRequ] => * [optWith] => [detaildesc] => Compute PDDT score matrix and substitute it as the sample correlation structure ) [sampvar] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sampvar [longAname] => [shortAname] => [shortName] => -h [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Load an alternative phenotype that alternates phenotype included in input, using assigned path [optExcl] => --simtrio [optRequ] => * [optWith] => * [detaildesc] => Load an alternative phenotype that alternates phenotype included in input, using assigned path ) [sampvarflag] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sampvarflag [longAname] => [shortAname] => [shortName] => -ai [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Sample variable reading flags ) [variantvar] => Array ( [is_given_default] => false [is_essential] => false [longName] => --variantvar [longAname] => [shortAname] => [shortName] => -a [defVal] => [optType] => a file path of variant variables [optCat] => RT_OTHER [desc] => Load the variables for variants in the dataset, used in the filtering/retrieving and annotation. [optExcl] => --vcf [optRequ] => * [optWith] => [detaildesc] => Load the variables for variants in the dataset, used in the filtering/retrieving and annotation. ) [filvariant] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filvariant [longAname] => [shortAname] => [shortName] => -fk [defVal] => [optType] => expression [optCat] => RT_OTHER [desc] => Filtering out variants which satisfies given condition. Conditions must be valid for the fields in VCF file or variant variable file. [optExcl] => --incvariant [optRequ] => --variantvar/--vcf [optWith] => [detaildesc] => Filtering out variants which satisfies given condition. Conditions must be valid for the fields in VCF file or variant variable file. ) [incvariant] => Array ( [is_given_default] => false [is_essential] => false [longName] => --incvariant [longAname] => [shortAname] => [shortName] => -ik [defVal] => [optType] => expression [optCat] => RT_OTHER [desc] => Retrieving only the variants which satisfies given condition. Conditions must be valid for the fields in VCF file or variant variable file. [optExcl] => --filvariant [optRequ] => --variantvar/--vcf [optWith] => [detaildesc] => Retrieving only the variants which satisfies given condition. Conditions must be valid for the fields in VCF file or variant variable file. ) [filgeno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filgeno [longAname] => [shortAname] => [shortName] => -fj [defVal] => [optType] => expression [optCat] => RT_OTHER [desc] => Filtering out genotypes which satisfies given condition. Conditions must be valid for the fields in VCF file. [optExcl] => --incgeno [optRequ] => --vcf [optWith] => [detaildesc] => Filtering out genotypes which satisfies given condition. Conditions must be valid for the fields in VCF file. ) [incgeno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --incgeno [longAname] => [shortAname] => [shortName] => -ij [defVal] => [optType] => expression [optCat] => RT_OTHER [desc] => Retrieving only the genotypes which satisfies given condition. Conditions must be valid for the fields in VCF file. [optExcl] => --filgeno [optRequ] => --vcf [optWith] => [detaildesc] => Retrieving only the genotypes which satisfies given condition. Conditions must be valid for the fields in VCF file. ) [pname] => Array ( [is_given_default] => false [is_essential] => false [longName] => --pname [longAname] => [shortAname] => [shortName] => -n [defVal] => * [optType] => string (comma[,] separated) [optCat] => RT_OTHER [desc] => Enumrate phenotype names that will be used in the analysis, comma(,) is a separator when the case of assignment of multiple phenotypes, and star(*) is an indicator that all phenotypes in the alternative phenotype file are used [optExcl] => * [optRequ] => --sampvar [optWith] => * [detaildesc] => Enumrate phenotype names that will be used in the analysis, comma(,) is a separator when the case of assignment of multiple phenotypes, and star(*) is an indicator that all phenotypes in the alternative phenotype file are used ) [corpair] => Array ( [is_given_default] => false [is_essential] => false [longName] => --corpair [longAname] => [shortAname] => [shortName] => -ca [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export sample relatedness matrix as paried form. One line consists of IIDs of two samples and their relaedness value [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export sample relatedness matrix as paried form. One line consists of IIDs of two samples and their relaedness value ) [corgrm] => Array ( [is_given_default] => false [is_essential] => false [longName] => --corgrm [longAname] => [shortAname] => [shortName] => -cg [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export sample relatedness matrix with binarized GRM format used in GCTA. [optExcl] => --corpair [optRequ] => * [optWith] => [detaildesc] => Export sample relatedness matrix with binarized GRM format used in GCTA. ) [corepacts] => Array ( [is_given_default] => false [is_essential] => false [longName] => --corepacts [longAname] => [shortAname] => [shortName] => -ep [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Export sample relatedness matrix with EPACTS kin format ) [remsamp] => Array ( [is_given_default] => false [is_essential] => false [longName] => --remsamp [longAname] => [shortAname] => [shortName] => -ir [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Exclude all samples listed in the assigned file from the analyses, based on the pair of FID and IID, or IID only [optExcl] => --selsamp [optRequ] => * [optWith] => * [detaildesc] => Exclude all samples listed in the assigned file from the analyses, based on the pair of FID and IID, or IID only ) [selsamp] => Array ( [is_given_default] => false [is_essential] => false [longName] => --selsamp [longAname] => [shortAname] => [shortName] => -is [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Include only the samples listed in the assigned file from the analyses, based on the pair of FID and IID, or IID only [optExcl] => --remsamp [optRequ] => * [optWith] => * [detaildesc] => Include only the samples listed in the assigned file from the analyses, based on the pair of FID and IID, or IID only ) [nasamp] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nasamp [longAname] => [shortAname] => [shortName] => -xs [defVal] => [optType] => Single IID or multiple IIDs separated by comma(,) white no whitespace [optCat] => RT_OTHER [desc] => Blow out the genotype of chosen samples, can be file path containing FID & IID pair or list of IIDs divided by comma(,) with no whitespace. [optExcl] => --randnasamp [optRequ] => * [optWith] => [detaildesc] => Blow out the genotype of chosen samples, can be file path containing FID & IID pair or list of IIDs divided by comma(,) with no whitespace. ) [randnasamp] => Array ( [is_given_default] => false [is_essential] => false [longName] => --randnasamp [longAname] => [shortAname] => [shortName] => -rx [defVal] => [optType] => A real number between 0 and 1, or positive integer [optCat] => RT_PROPNUM [desc] => If argument is integer and over 1, the number of samples are randomly chosen and blowed out their genotype. If the number is betwen 0 and 1, it interpreted as 'proportion'. [optExcl] => --nasamp [optRequ] => * [optWith] => [detaildesc] => If argument is integer and over 1, the number of samples are randomly chosen and blowed out their genotype. If the number is betwen 0 and 1, it interpreted as 'proportion'. ) [remvariant] => Array ( [is_given_default] => false [is_essential] => false [longName] => --remvariant [longAname] => [shortAname] => [shortName] => -sr [defVal] => [optType] => Variant IDs divided by comma(,) w/o whitespace or file path [optCat] => RT_OTHER [desc] => Removing variants in the dataset from the argument, or from the given file. [optExcl] => --nomap [optRequ] => * [optWith] => * [detaildesc] => Removing variants in the dataset from the argument, or from the given file. ) [selvariant] => Array ( [is_given_default] => false [is_essential] => false [longName] => --selvariant [longAname] => [shortAname] => [shortName] => -Ss [defVal] => [optType] => Variant IDs divided by comma(,) w/o whitespace or file path [optCat] => RT_OTHER [desc] => Selecting variants in the dataset from the argument, or from the given file. [optExcl] => --nomap [optRequ] => * [optWith] => * [detaildesc] => Selecting variants in the dataset from the argument, or from the given file. ) [remfam] => Array ( [is_given_default] => false [is_essential] => false [longName] => --remfam [longAname] => [shortAname] => [shortName] => -fF [defVal] => 0 [optType] => FIDs(divided by comma[,]) or file path [optCat] => RT_OTHER [desc] => Exclude all samples having its FID in the argument. Argument can be the path of file contains FIDs to be included, or FIDs divided by comma[,] with no whitespaces [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Exclude all samples having its FID in the argument. Argument can be the path of file contains FIDs to be included, or FIDs divided by comma[,] with no whitespaces ) [selfam] => Array ( [is_given_default] => false [is_essential] => false [longName] => --selfam [longAname] => [shortAname] => [shortName] => -iF [defVal] => 0 [optType] => FIDs(divided by comma[,]) or file path [optCat] => RT_OTHER [desc] => Include only the samples having its FID in the argument. Argument can be the path of file contains FIDs to be included, or FIDs divided by comma[,] with no whitespaces [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Include only the samples having its FID in the argument. Argument can be the path of file contains FIDs to be included, or FIDs divided by comma[,] with no whitespaces ) [filrange] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filrange [longAname] => [shortAname] => [shortName] => -rr [defVal] => [optType] => a path of file consisting 3 columns(chromosome, start, end) [optCat] => RT_OTHER [desc] => Filtering out variant if the physical position of variant resides in given range in the file. [optExcl] => --nomap [optRequ] => * [optWith] => * [detaildesc] => Filtering out variant if the physical position of variant resides in given range in the file. ) [incrange] => Array ( [is_given_default] => false [is_essential] => false [longName] => --incrange [longAname] => [shortAname] => [shortName] => -rs [defVal] => [optType] => a path of file consisting 3 columns(chromosome, start, end) [optCat] => RT_OTHER [desc] => Selecting only variants if the physical position of variant resides in given range in the file. [optExcl] => --nomap [optRequ] => * [optWith] => * [detaildesc] => Selecting only variants if the physical position of variant resides in given range in the file. ) [varresize] => Array ( [is_given_default] => false [is_essential] => false [longName] => --varresize [longAname] => [shortAname] => [shortName] => -sz [defVal] => 0 [optType] => Positive integer(number of variants) or real number (0,1) (proportion of variants) [optCat] => RT_PROPNUM [desc] => Resizing the number of variants in the dataset by randomly selecting variants. When the argument is positive integer, corresponding number of variants will be chosen. Otherwise the argument is real number between 0 and 1, corresponding proportion of variants will be chosen. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Resizing the number of variants in the dataset by randomly selecting variants. When the argument is positive integer, corresponding number of variants will be chosen. Otherwise the argument is real number between 0 and 1, corresponding proportion of variants will be chosen. ) [varwindow] => Array ( [is_given_default] => false [is_essential] => false [longName] => --varwindow [longAname] => [shortAname] => [shortName] => -vw [defVal] => 0 [optType] => OT_NUMBER [optCat] => RT_POS [desc] => Size of variant-thinning window ) [sampresize] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sampresize [longAname] => [shortAname] => [shortName] => -az [defVal] => 0 [optType] => positive integer (>0) [optCat] => RT_PROPNUM [desc] => Randomly resizing samples into given number. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Randomly resizing samples into given number. ) [emcount] => Array ( [is_given_default] => false [is_essential] => false [longName] => --emcount [longAname] => [shortAname] => [shortName] => -ec [defVal] => 5 [optType] => positive integer [optCat] => RT_NONNEG [desc] => Determine the count of EM iteration in the analysis using EM-AI algorithm [optExcl] => * [optRequ] => --scoretest/--heritability [optWith] => * [detaildesc] => Determine the count of EM iteration in the analysis using EM-AI algorithm ) [aithr] => Array ( [is_given_default] => false [is_essential] => false [longName] => --aithr [longAname] => [shortAname] => [shortName] => -at [defVal] => 1e-8 [optType] => real number (0~1) [optCat] => RT_POS [desc] => Determine the convergence threshold of AI iteration in the analysis using EM-AI algorithm [optExcl] => * [optRequ] => --scoretest/--heritability [optWith] => * [detaildesc] => Determine the convergence threshold of AI iteration in the analysis using EM-AI algorithm ) [autoonly] => Array ( [is_given_default] => false [is_essential] => false [longName] => --autoonly [longAname] => [shortAname] => [shortName] => -U [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Include only the autosomes in the analyses, i.e., exclude all non-autosome variants including unmapped and sex chromosome variants [optExcl] => --sexonly,--nomap [optRequ] => * [optWith] => * [detaildesc] => Include only the autosomes in the analyses, i.e., exclude all non-autosome variants including unmapped and sex chromosome variants ) [sexonly] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sexonly [longAname] => [shortAname] => [shortName] => -sx [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Includy only the sex chromosomes in the analyses, i.e., exclude all non-sex chromosome variants [optExcl] => --autoonly [optRequ] => * [optWith] => * [detaildesc] => Includy only the sex chromosomes in the analyses, i.e., exclude all non-sex chromosome variants ) [chr] => Array ( [is_given_default] => false [is_essential] => false [longName] => --chr [longAname] => [shortAname] => [shortName] => -ch [defVal] => [optType] => 1~22, X, Y [optCat] => RT_OTHER [desc] => Include only the chromosomes listed in the argument, an assignment of multiple chromosomes should be divided with comma(,) with no space. Note that using of --autoonly with this option with arguments including sex chromosomes will produce error [optExcl] => --nomap [optRequ] => * [optWith] => * [detaildesc] => Include only the chromosomes listed in the argument, an assignment of multiple chromosomes should be divided with comma(,) with no space. Note that using of --autoonly with this option with arguments including sex chromosomes will produce error ) [freq] => Array ( [is_given_default] => false [is_essential] => false [longName] => --freq [longAname] => [shortAname] => [shortName] => -f [defVal] => founder [optType] => all / founder / corr [optCat] => RT_OTHER [desc] => Compute and export minor-allele frequency for each variant. Samples included to get MAF will vary on the parameter [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Compute and export minor-allele frequency for each variant. Samples included to get MAF will vary on the parameter ) [hwe] => Array ( [is_given_default] => false [is_essential] => false [longName] => --hwe [longAname] => [shortAname] => [shortName] => -H [defVal] => founder [optType] => all / founder / corr(Not implemented) [optCat] => RT_OTHER [desc] => Compute and export the result of Hardy-Weinberg Equilibrium test. Samples included to perform test will vart on the parameter [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Compute and export the result of Hardy-Weinberg Equilibrium test. Samples included to perform test will vart on the parameter ) [makeblup] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makeblup [longAname] => [shortAname] => [shortName] => -mu [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export BLUP value of all given phenotypes after LMM fitting [optExcl] => * [optRequ] => --scoretest/--heritability [optWith] => * [detaildesc] => Export BLUP value of all given phenotypes after LMM fitting ) [filmaf] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filmaf [longAname] => [shortAname] => [shortName] => -ff [defVal] => [optType] => OT_RANGE [optCat] => RT_01 [desc] => Filtering out variants by minor allele frequency ) [filmac] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filmac [longAname] => [shortAname] => [shortName] => -fm [defVal] => [optType] => range (0~1) [optCat] => RT_NONNEG [desc] => Exclude all variants having its number of minor alleles in specified range [optExcl] => --incmac [optRequ] => * [optWith] => --window [detaildesc] => Exclude all variants having its number of minor alleles in specified range ) [filhwe] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filhwe [longAname] => [shortAname] => [shortName] => -fh [defVal] => [optType] => range (0~1) [optCat] => RT_01 [desc] => Exclude all variants having its p-value of Hardy-Weinberg Equilibrium test in specified range [optExcl] => --inchwe [optRequ] => --hwe,--hwe≠corr [optWith] => --window [detaildesc] => Exclude all variants having its p-value of Hardy-Weinberg Equilibrium test in specified range ) [filgind] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filgind [longAname] => [shortAname] => [shortName] => -fg [defVal] => [optType] => range (0~1) [optCat] => RT_01 [desc] => Exclude all samples having its genotyping rate in specified range [optExcl] => --incgind [optRequ] => * [optWith] => * [detaildesc] => Exclude all samples having its genotyping rate in specified range ) [filgvar] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filgvar [longAname] => [shortAname] => [shortName] => -fp [defVal] => [optType] => range (0~1) [optCat] => RT_01 [desc] => Exclude all variants having its genotyping rate in specified range [optExcl] => --incgvar [optRequ] => * [optWith] => --window [detaildesc] => Exclude all variants having its genotyping rate in specified range ) [filnf] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filnf [longAname] => [shortAname] => [shortName] => -fN [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Exclude all non-founder samples from analyses [optExcl] => --nofam,--noparent [optRequ] => * [optWith] => * [detaildesc] => Exclude all non-founder samples from analyses ) [filmf] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filmf [longAname] => [shortAname] => [shortName] => -fs [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Filtering out all missing founder samples from the analyses [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Filtering out all missing founder samples from the analyses ) [filcase] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filcase [longAname] => [shortAname] => [shortName] => -fa [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Exclude case samples from analyses [optExcl] => * [optRequ] => [Binary trait] [optWith] => * [detaildesc] => Exclude case samples from analyses ) [filcontrol] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filcontrol [longAname] => [shortAname] => [shortName] => -ft [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Exclude control samples from analyses [optExcl] => * [optRequ] => [Binary trait] [optWith] => * [detaildesc] => Exclude control samples from analyses ) [filmispheno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filmispheno [longAname] => [shortAname] => [shortName] => -fo [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Filtering out all samples having missing phenotype. If there are alternative phenotype or multiple phenotype, all samples having AT LEAST one missing will be filtered out. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Filtering out all samples having missing phenotype. If there are alternative phenotype or multiple phenotype, all samples having AT LEAST one missing will be filtered out. ) [filsample] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filsample [longAname] => [shortAname] => [shortName] => -fn [defVal] => [optType] => expression [optCat] => RT_OTHER [desc] => Filtering out all samples satisfying given condition. The condition should be a valid expression for sample variable. [optExcl] => --incsample [optRequ] => --sampvar [optWith] => [detaildesc] => Filtering out all samples satisfying given condition. The condition should be a valid expression for sample variable. ) [filgdist] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filgdist [longAname] => [shortAname] => [shortName] => -fi [defVal] => [optType] => range [optCat] => RT_NONNEG [desc] => Exclude all variants satisfying the condition that its genetic distance in given range [optExcl] => --incgdist,--nomap [optRequ] => * [optWith] => --window [detaildesc] => Exclude all variants satisfying the condition that its genetic distance in given range ) [filnosex] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filnosex [longAname] => [shortAname] => [shortName] => -fx [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Exclude all samples who missing their sex information [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Exclude all samples who missing their sex information ) [filmale] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filmale [longAname] => [shortAname] => [shortName] => -fl [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Exclude all male samples from subsequent analyses [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Exclude all male samples from subsequent analyses ) [filfemale] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filfemale [longAname] => [shortAname] => [shortName] => -fe [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Exclude all female samples from subsequent analyses [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Exclude all female samples from subsequent analyses ) [snvonly] => Array ( [is_given_default] => false [is_essential] => false [longName] => --snvonly [longAname] => [shortAname] => [shortName] => -vo [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Filtering out all variants if they are not SNV. i.e., filtering out the makrer if its major/minor allele is not a locus [optExcl] => --indelonly [optRequ] => * [optWith] => * [detaildesc] => Filtering out all variants if they are not SNV. i.e., filtering out the makrer if its major/minor allele is not a locus ) [indelonly] => Array ( [is_given_default] => false [is_essential] => false [longName] => --indelonly [longAname] => [shortAname] => [shortName] => -xo [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Filtering out all variants if they are SNV. i.e., filtering out the variant if its major and minor allele are all a single locus. [optExcl] => --snvonly[RAW file] [optRequ] => * [optWith] => * [detaildesc] => Filtering out all variants if they are SNV. i.e., filtering out the variant if its major and minor allele are all a single locus. ) [incmaf] => Array ( [is_given_default] => false [is_essential] => false [longName] => --incmaf [longAname] => [shortAname] => [shortName] => -if [defVal] => [optType] => OT_RANGE [optCat] => RT_01 [desc] => Including variants by minor allele frequency ) [incmac] => Array ( [is_given_default] => false [is_essential] => false [longName] => --incmac [longAname] => [shortAname] => [shortName] => -im [defVal] => [optType] => range (0~1) [optCat] => RT_NONNEG [desc] => Include only the variants having its number of minor alleles in specified range [optExcl] => --filmac [optRequ] => * [optWith] => * [detaildesc] => Include only the variants having its number of minor alleles in specified range ) [inchwe] => Array ( [is_given_default] => false [is_essential] => false [longName] => --inchwe [longAname] => [shortAname] => [shortName] => -ih [defVal] => [optType] => range (0~1) [optCat] => RT_01 [desc] => Include the variants to the analyses only that having its p-value of Hardy-Weinberg Equilibrium test in specified range [optExcl] => --filhwe [optRequ] => * [optWith] => * [detaildesc] => Include the variants to the analyses only that having its p-value of Hardy-Weinberg Equilibrium test in specified range ) [incgind] => Array ( [is_given_default] => false [is_essential] => false [longName] => --incgind [longAname] => [shortAname] => [shortName] => -ig [defVal] => [optType] => range (0~1) [optCat] => RT_01 [desc] => Include only the samples having its genotyping rate in speicifed range [optExcl] => --filgind [optRequ] => * [optWith] => * [detaildesc] => Include only the samples having its genotyping rate in speicifed range ) [incgvar] => Array ( [is_given_default] => false [is_essential] => false [longName] => --incgvar [longAname] => [shortAname] => [shortName] => -iv [defVal] => [optType] => range (0~1) [optCat] => RT_01 [desc] => Include only the variants having its genotyping rate in specified range [optExcl] => --filgvar [optRequ] => * [optWith] => * [detaildesc] => Include only the variants having its genotyping rate in specified range ) [incgdist] => Array ( [is_given_default] => false [is_essential] => false [longName] => --incgdist [longAname] => [shortAname] => [shortName] => -ii [defVal] => [optType] => range [optCat] => RT_NONNEG [desc] => Include only the variants satisfying the condition that its genetic distance in given range [optExcl] => --filgdist,--nomap [optRequ] => * [optWith] => * [detaildesc] => Include only the variants satisfying the condition that its genetic distance in given range ) [incsample] => Array ( [is_given_default] => false [is_essential] => false [longName] => --incsample [longAname] => [shortAname] => [shortName] => -in [defVal] => [optType] => expression [optCat] => RT_OTHER [desc] => Selecting samples only satisfying given condition. The condition should be a valid expression for sample variable. [optExcl] => --filsample [optRequ] => --sampvar [optWith] => [detaildesc] => Selecting samples only satisfying given condition. The condition should be a valid expression for sample variable. ) [set] => Array ( [is_given_default] => false [is_essential] => false [longName] => --set [longAname] => [shortAname] => [shortName] => -s [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Load a set includes gene-set definition from assigned path [optExcl] => --setconsec,--setoverlap [optRequ] => * [optWith] => * [detaildesc] => Load a set includes gene-set definition from assigned path ) [scoretest] => Array ( [is_given_default] => false [is_essential] => false [longName] => --scoretest [longAname] => [shortAname] => [shortName] => -ct [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform variant-level score test (both for Rao's score test and Generalizaed score test) [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Perform variant-level score test (both for Rao's score test and Generalizaed score test) ) [heritability] => Array ( [is_given_default] => false [is_essential] => false [longName] => --heritability [longAname] => [shortAname] => [shortName] => -he [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform the analysis of estimated heritability based on the phenotypes and given family structure [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Perform the analysis of estimated heritability based on the phenotypes and given family structure ) [ml] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ml [longAname] => [shortAname] => [shortName] => -ml [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Use ML(Maximum likelihood) method instead of REML(REstricted Maximum Likelihood) method, when perform score test. Some score tests that REML cannot be applied will automatically use ML method regardless of the presence of this option [optExcl] => * [optRequ] => --scoretest/--heritability/--gemma [optWith] => [detaildesc] => Use ML(Maximum likelihood) method instead of REML(REstricted Maximum Likelihood) method, when perform score test. Some score tests that REML cannot be applied will automatically use ML method regardless of the presence of this option ) [blup] => Array ( [is_given_default] => false [is_essential] => false [longName] => --blup [longAname] => [shortAname] => [shortName] => -b [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => In case of determining phenotype, set the final phenotype value as the subtraction from given phenotype to BLUP value in the assigned path. Note that the dataset used to compute BLUP and target dataset should be identical, and also if the given phenotype is dichotomous(binary) phenotype, it will be considered as continuous phenotype [optExcl] => * [optRequ] => * [optWith] => --scoretest/--heritability/--gmdr [detaildesc] => In case of determining phenotype, set the final phenotype value as the subtraction from given phenotype to BLUP value in the assigned path. Note that the dataset used to compute BLUP and target dataset should be identical, and also if the given phenotype is dichotomous(binary) phenotype, it will be considered as continuous phenotype ) [prevalence] => Array ( [is_given_default] => false [is_essential] => false [longName] => --prevalence [longAname] => [shortAname] => [shortName] => -pv [defVal] => [optType] => real number(0~1),two real number(0~1),multiple real number(0~1) [optCat] => RT_OTHER [desc] => Set the prevalence of disease, for the analyses requiring that. Two prevalences separated comma(,) with no whitespace are allowed in univariate case, to assign separate prevalences for male and female, respectively. In case of multivariate case, the number of prevalences MUST be same with the number of phenotypes analyzed. [optExcl] => * [optRequ] => --genetest/--fqls [optWith] => * [detaildesc] => Set the prevalence of disease, for the analyses requiring that. Two prevalences separated comma(,) with no whitespace are allowed in univariate case, to assign separate prevalences for male and female, respectively. In case of multivariate case, the number of prevalences MUST be same with the number of phenotypes analyzed. ) [medcor] => Array ( [is_given_default] => false [is_essential] => false [longName] => --medcor [longAname] => [shortAname] => [shortName] => -Mc [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Compute empirical correlation based on the median of observed value, instead of mean of observed values [optExcl] => --hybrid,--indep,--corpearson,--pddt,--ibs,--ktau,--empktau,--empiall,--cor [optRequ] => * [optWith] => * [detaildesc] => Compute empirical correlation based on the median of observed value, instead of mean of observed values ) [imputepheno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --imputepheno [longAname] => [shortAname] => [shortName] => -ip [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Substitute the phenotype to 0 if it is missing, just in case of gene-level analysis of dichotomous univariate phenotype with the assignment of --prevalence [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Substitute the phenotype to 0 if it is missing, just in case of gene-level analysis of dichotomous univariate phenotype with the assignment of --prevalence ) [cname] => Array ( [is_given_default] => false [is_essential] => false [longName] => --cname [longAname] => [shortAname] => [shortName] => -cn [defVal] => [optType] => string (comma[,] separated) [optCat] => RT_OTHER [desc] => Enumrate covariate names that will be used in the analysis, comma(,) is a separator when the case of assignment of multiple covariates, and star(*) is an indicator that all phenotypes in the alternative phenotype file are used [optExcl] => * [optRequ] => --sampvar [optWith] => * [detaildesc] => Enumrate covariate names that will be used in the analysis, comma(,) is a separator when the case of assignment of multiple covariates, and star(*) is an indicator that all phenotypes in the alternative phenotype file are used ) [cor] => Array ( [is_given_default] => false [is_essential] => false [longName] => --cor [longAname] => [shortAname] => [shortName] => -c [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Load the sample correlation structure from assigned path, instead of computing sample correlation structure directly. Note that the number of samples in the file must match with the number of samples in the final dataset. If the assigned input is not 3-column format, the sequence of samples also must match [optExcl] => --hybrid,--indep,--corpearson,--pddt,--ibs,--ktau,--empktau,--empiall,--medcor [optRequ] => * [optWith] => * [detaildesc] => Load the sample correlation structure from assigned path, instead of computing sample correlation structure directly. Note that the number of samples in the file must match with the number of samples in the final dataset. If the assigned input is not 3-column format, the sequence of samples also must match ) [makecor] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makecor [longAname] => [shortAname] => [shortName] => -MC [defVal] => default [optType] => [optCat] => RT_OTHER [desc] => Export computed/imported sample relatedness matrix [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Export computed/imported sample relatedness matrix ) [cordiag1] => Array ( [is_given_default] => false [is_essential] => false [longName] => --cordiag1 [longAname] => [shortAname] => [shortName] => -cd [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Force the diagonal term of the sample correlation structure to be 1 if the value is less than 1. This option will not affect to the off-diagonal term [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Force the diagonal term of the sample correlation structure to be 1 if the value is less than 1. This option will not affect to the off-diagonal term ) [empiall] => Array ( [is_given_default] => false [is_essential] => false [longName] => --empiall [longAname] => [shortAname] => [shortName] => -ea [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Compute empirical kinship matrix, with all available samples instead of founder samples [optExcl] => --hybrid,--corpearson,--cor,--pddt,--ibs,--ktau,--empktau,--indep,--medcor [optRequ] => * [optWith] => * [detaildesc] => Compute empirical kinship matrix, with all available samples instead of founder samples ) [corpearson] => Array ( [is_given_default] => false [is_essential] => false [longName] => --corpearson [longAname] => [shortAname] => [shortName] => -cp [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Compute Pearson's correlation coefficient across all samples based on the genotype, and substitute it as the sample correlation matrix [optExcl] => --indep,--cor,--pddt,--ibs,--ktau,--empktau,--empiall,--medcor [optRequ] => * [optWith] => * [detaildesc] => Compute Pearson's correlation coefficient across all samples based on the genotype, and substitute it as the sample correlation matrix ) [indep] => Array ( [is_given_default] => false [is_essential] => false [longName] => --indep [longAname] => [shortAname] => [shortName] => -id [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Force all samples in the dataset to be independent, i.e., make the sample correlation structure to identity matrix [optExcl] => --hybrid,--corpearson,--cor,--pddt,--ibs,--ktau,--empktau,--empiall,--medcor [optRequ] => * [optWith] => * [detaildesc] => Force all samples in the dataset to be independent, i.e., make the sample correlation structure to identity matrix ) [mispheno] => Array ( [is_given_default] => true [is_essential] => false [longName] => --mispheno [longAname] => [shortAname] => [shortName] => -mh [defVal] => -9 [optType] => string [optCat] => RT_OTHER [desc] => Set a string that indicates missing value against the phenotype included in the input, and phenotypes/covariates from the alternative phenotype file used in the analysis. Any non-whitespace sequence of ascii characters allowed. [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Set a string that indicates missing value against the phenotype included in the input, and phenotypes/covariates from the alternative phenotype file used in the analysis. Any non-whitespace sequence of ascii characters allowed. ) [misgeno] => Array ( [is_given_default] => true [is_essential] => false [longName] => --misgeno [longAname] => [shortAname] => [shortName] => -mg [defVal] => 0 [optType] => string [optCat] => RT_OTHER [desc] => Set a character or string for the representation of "genotype missingness". Any non-whitespace sequence of ascii characters allowed. [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Set a character or string for the representation of "genotype missingness". Any non-whitespace sequence of ascii characters allowed. ) [1case] => Array ( [is_given_default] => true [is_essential] => false [longName] => --1case [longAname] => [shortAname] => [shortName] => -x1 [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Change an indicator of binary phenotype from default, 2(case)/1(control) to 1(case)/0(control) [optExcl] => --cact [optRequ] => * [optWith] => * [detaildesc] => Change an indicator of binary phenotype from default, 2(case)/1(control) to 1(case)/0(control) ) [cact] => Array ( [is_given_default] => false [is_essential] => false [longName] => --cact [longAname] => [shortAname] => [shortName] => -cc [defVal] => [optType] => two integers separated by comma(,) with no whitespace [optCat] => RT_OTHER [desc] => Sequentially assign two integer value represents case and control phenotype, respectively. Only the two integers divided by comma[,] with NO whitespaces are allowed. [optExcl] => --1case [optRequ] => * [optWith] => * [detaildesc] => Sequentially assign two integer value represents case and control phenotype, respectively. Only the two integers divided by comma[,] with NO whitespaces are allowed. ) [1sex] => Array ( [is_given_default] => true [is_essential] => false [longName] => --1sex [longAname] => [shortAname] => [shortName] => -s1 [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Set 1=female and 0=male for sex coding. [optExcl] => --mafe [optRequ] => * [optWith] => [detaildesc] => Set 1=female and 0=male for sex coding. ) [mafe] => Array ( [is_given_default] => false [is_essential] => false [longName] => --mafe [longAname] => [shortAname] => [shortName] => -MF [defVal] => [optType] => Two strings separated with comma(,) with no whitespaces [optCat] => RT_OTHER [desc] => Set male and female coding for input, respectively. [optExcl] => --1sex [optRequ] => * [optWith] => [detaildesc] => Set male and female coding for input, respectively. ) [ginv] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ginv [longAname] => [shortAname] => [shortName] => -gi [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Utilize Generalized inverse method if traditional method failed. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Utilize Generalized inverse method if traditional method failed. ) [makecov] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makecov [longAname] => [shortAname] => [shortName] => -mc [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export processed and filtered covariates information to file [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export processed and filtered covariates information to file ) [makepheno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makepheno [longAname] => [shortAname] => [shortName] => -mP [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export samples and their phenotype values in the final dataset [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export samples and their phenotype values in the final dataset ) [makeflag] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makeflag [longAname] => [shortAname] => [shortName] => -Mf [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Flags for generating sample-based output files ) [bim] => Array ( [is_given_default] => false [is_essential] => false [longName] => --bim [longAname] => [shortAname] => [shortName] => -bi [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Use assigned path to load bim file when BED file has assigned as an input [optExcl] => * [optRequ] => --bed [optWith] => [detaildesc] => Use assigned path to load bim file when BED file has assigned as an input ) [founderonly] => Array ( [is_given_default] => false [is_essential] => false [longName] => --founderonly [longAname] => [shortAname] => [shortName] => -Fo [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Using only founder samples in LD computation and sample relatedness estimation [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Using only founder samples in LD computation and sample relatedness estimation ) [famsummary] => Array ( [is_given_default] => false [is_essential] => false [longName] => --famsummary [longAname] => [shortAname] => [shortName] => -Fs [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Produce a report about the family structure based on their FID [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Produce a report about the family structure based on their FID ) [ncsummary] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ncsummary [longAname] => [shortAname] => [shortName] => -nc [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Produce a report about the nuclear families based on their pedigree structure [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Produce a report about the nuclear families based on their pedigree structure ) [ibs] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ibs [longAname] => [shortAname] => [shortName] => -bs [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Compute IBS score matrix, and substitute it as the sample correlation structure. Note that it will not working properly against rare-varaint only dataset [optExcl] => --hybrid,--corpearson,--cor,--pddt,--indep,--ktau,--empktau,--empiall,--medcor [optRequ] => * [optWith] => [detaildesc] => Compute IBS score matrix, and substitute it as the sample correlation structure. Note that it will not working properly against rare-varaint only dataset ) [seed] => Array ( [is_given_default] => false [is_essential] => false [longName] => --seed [longAname] => [shortAname] => [shortName] => -S [defVal] => [optType] => positive integer [optCat] => RT_NUM [desc] => Force the random seed. Can be utilized to replication [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Force the random seed. Can be utilized to replication ) [map] => Array ( [is_given_default] => false [is_essential] => false [longName] => --map [longAname] => [shortAname] => [shortName] => -M [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Use assigned path to load map file when PED file has assigned as an input [optExcl] => * [optRequ] => --ped/--lgen [optWith] => [detaildesc] => Use assigned path to load map file when PED file has assigned as an input ) [specdcmp] => Array ( [is_given_default] => false [is_essential] => false [longName] => --specdcmp [longAname] => [shortAname] => [shortName] => -sd [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Use spectral decomposition method instead of EM-AI algorithm in the analyses utilizing Linear Mixed Model [optExcl] => --nospecdcmp [optRequ] => --scoretest/--heritability [optWith] => [detaildesc] => Use spectral decomposition method instead of EM-AI algorithm in the analyses utilizing Linear Mixed Model ) [runas] => Array ( [is_given_default] => false [is_essential] => false [longName] => --runas [longAname] => [shortAname] => [shortName] => -r [defVal] => 0 [optType] => file path [optCat] => RT_OTHER [desc] => Run WISARD based on an assigned path. Note that the arguments assigned with this option will affect regardless of duplication. Following file can be accepted as a valid input. 1) A log file produced from WISARD, 2) A file includes valid options [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Run WISARD based on an assigned path. Note that the arguments assigned with this option will affect regardless of duplication. Following file can be accepted as a valid input. 1) A log file produced from WISARD, 2) A file includes valid options ) [nostop] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nostop [longAname] => [shortAname] => [shortName] => -xx [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Do not break up AI iteration until the convergence threshold is satisfied in AI algorithm [optExcl] => * [optRequ] => --scoretest/--heritability [optWith] => [detaildesc] => Do not break up AI iteration until the convergence threshold is satisfied in AI algorithm ) [x] => Array ( [is_given_default] => false [is_essential] => false [longName] => --x [longAname] => [shortAname] => [shortName] => -x [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Compute PDDT with an assumption of X chromosome [optExcl] => * [optRequ] => --pddt [optWith] => [detaildesc] => Compute PDDT with an assumption of X chromosome ) [x2] => Array ( [is_given_default] => false [is_essential] => false [longName] => --x2 [longAname] => [shortAname] => [shortName] => -x2 [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Compute the theoretical kinship coefficient under X chromosome assmption(with --kinship) or convert empirical sample relatedness matrix with autosomes into X chromosome-compatible sample relatedness matrix for the statistics of X-chromosome. [optExcl] => --x [optRequ] => * [optWith] => [detaildesc] => Compute the theoretical kinship coefficient under X chromosome assmption(with --kinship) or convert empirical sample relatedness matrix with autosomes into X chromosome-compatible sample relatedness matrix for the statistics of X-chromosome. ) [ignoreparent] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ignoreparent [longAname] => [shortAname] => [shortName] => -Ip [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Ignore parent field of pedigree information and treat them as founders [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Ignore parent field of pedigree information and treat them as founders ) [ignorefid] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ignorefid [longAname] => [shortAname] => [shortName] => -If [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Ignore FID of pedigree information but does not ignore parent field, thus be aware of error! [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Ignore FID of pedigree information but does not ignore parent field, thus be aware of error! ) [nofid] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nofid [longAname] => [shortAname] => [shortName] => -Nf [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Let WISARD to assume there is no FID field [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Let WISARD to assume there is no FID field ) [sepid] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sepid [longAname] => [shortAname] => [shortName] => -Si [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Assume there is a separator between FID and IID rather than whitespace ) [noparent] => Array ( [is_given_default] => false [is_essential] => false [longName] => --noparent [longAname] => [shortAname] => [shortName] => -np [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Let WISARD to assume there is no PAT and MAT field that indicates parental relationship [optExcl] => --filnf,--misparent [optRequ] => * [optWith] => [detaildesc] => Let WISARD to assume there is no PAT and MAT field that indicates parental relationship ) [nosex] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nosex [longAname] => [shortAname] => [shortName] => -nX [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Assume there is no column for sex in the six-column mandatory pedigree definition [optExcl] => --filmale,--filfemale,--filnosex [optRequ] => * [optWith] => * [detaildesc] => Assume there is no column for sex in the six-column mandatory pedigree definition ) [nopheno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nopheno [longAname] => [shortAname] => [shortName] => -nP [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Assume there is no column for phenotype in the six-column mandatory pedigree definition [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Assume there is no column for phenotype in the six-column mandatory pedigree definition ) [nopos] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nopos [longAname] => [shortAname] => [shortName] => -no [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => When loading variant description file for given input, assume there is no column for physical position of variant. [optExcl] => --nomap [optRequ] => * [optWith] => [detaildesc] => When loading variant description file for given input, assume there is no column for physical position of variant. ) [nogdist] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nogdist [longAname] => [shortAname] => [shortName] => -ng [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => When loading variant description file for given input, assume there is no column for genetic distance of variant. [optExcl] => --nomap [optRequ] => * [optWith] => [detaildesc] => When loading variant description file for given input, assume there is no column for genetic distance of variant. ) [probandcol] => Array ( [is_given_default] => false [is_essential] => false [longName] => --probandcol [longAname] => [shortAname] => [shortName] => -pb [defVal] => [optType] => string with no whitespace [optCat] => RT_OTHER [desc] => Assign the column name representing proband information. Note that the default value for the column name for proband is 'PROBAND' and this name is reserved [optExcl] => * [optRequ] => --sampvar [optWith] => [detaildesc] => Assign the column name representing proband information. Note that the default value for the column name for proband is 'PROBAND' and this name is reserved ) [twincol] => Array ( [is_given_default] => false [is_essential] => false [longName] => --twincol [longAname] => [shortAname] => [shortName] => -tw [defVal] => [optType] => string with no whitespace [optCat] => RT_OTHER [desc] => Assign the column name representing twin information. Twin information is an integer and each twin must have same and unique integer for them. Note that the default value for the column name for twin is 'TWIN' and this name is reserved [optExcl] => * [optRequ] => --sampvar [optWith] => [detaildesc] => Assign the column name representing twin information. Twin information is an integer and each twin must have same and unique integer for them. Note that the default value for the column name for twin is 'TWIN' and this name is reserved ) [noweight] => Array ( [is_given_default] => false [is_essential] => false [longName] => --noweight [longAname] => [shortAname] => [shortName] => -ew [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Let the analyses using variant-level weight do not apply weights. [optExcl] => --weight,--mafweight,--betaweight [optRequ] => * [optWith] => * [detaildesc] => Let the analyses using variant-level weight do not apply weights. ) [betaweight] => Array ( [is_given_default] => false [is_essential] => false [longName] => --betaweight [longAname] => [shortAname] => [shortName] => -bw [defVal] => 1,25 [optType] => [optCat] => RT_OTHER [desc] => Automatically generate a weight for variant based on the distribution of beta(1, 25) [optExcl] => --weight,--mafweight,--equalweight [optRequ] => * [optWith] => * [detaildesc] => Automatically generate a weight for variant based on the distribution of beta(1, 25) ) [mafweight] => Array ( [is_given_default] => false [is_essential] => false [longName] => --mafweight [longAname] => [shortAname] => [shortName] => -Mw [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Apply MAF-based inverse weight for all analyses requiring variant-wise weight. [optExcl] => --weight,--betaweight,--noweight [optRequ] => * [optWith] => [detaildesc] => Apply MAF-based inverse weight for all analyses requiring variant-wise weight. ) [hybrid] => Array ( [is_given_default] => false [is_essential] => false [longName] => --hybrid [longAname] => [shortAname] => [shortName] => -hy [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Compute hybrid score matrix and substitute it as the sample correlation structure. An element of hybrid score will have PDDT score if both samples have same FID, otherwise have empirical correlation [optExcl] => --ibs,--corpearson,--cor,--kinship,--indep,--ktau,--empktau,--empiall,--medcor [optRequ] => * [optWith] => [detaildesc] => Compute hybrid score matrix and substitute it as the sample correlation structure. An element of hybrid score will have PDDT score if both samples have same FID, otherwise have empirical correlation ) [gsmacthr] => Array ( [is_given_default] => false [is_essential] => false [longName] => --gsmacthr [longAname] => [shortAname] => [shortName] => -gt [defVal] => 0 [optType] => positive integer [optCat] => RT_NONNEG [desc] => Exclude all gene definitions do not satifies its sum of minor allele count(MAC) from the variants included [optExcl] => * [optRequ] => --genetest [optWith] => * [detaildesc] => Exclude all gene definitions do not satifies its sum of minor allele count(MAC) from the variants included ) [chrwise] => Array ( [is_given_default] => false [is_essential] => false [longName] => --chrwise [longAname] => [shortAname] => [shortName] => -cw [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Divide given input into chromosome, and perform analyses chromosome-wise. Note that the output also will be produced chromosome-wise [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Divide given input into chromosome, and perform analyses chromosome-wise. Note that the output also will be produced chromosome-wise ) [est] => Array ( [is_given_default] => false [is_essential] => false [longName] => --est [longAname] => [shortAname] => [shortName] => -E [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Load ".est" file produced from WISARD which including the output from EM-AI algorithm and utilize this information to analysis [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Load ".est" file produced from WISARD which including the output from EM-AI algorithm and utilize this information to analysis ) [weight] => Array ( [is_given_default] => false [is_essential] => false [longName] => --weight [longAname] => [shortAname] => [shortName] => -w [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Load user-defined weights. No missing or duplicated weight is allowed. [optExcl] => --equalweight,--betaweight,--mafweight [optRequ] => * [optWith] => [detaildesc] => Load user-defined weights. No missing or duplicated weight is allowed. ) [nomap] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nomap [longAname] => [shortAname] => [shortName] => -nm [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Proceed analyses regardless of presence of map file, variant name and position will be assigned arbitrary, so options related to chromosome, physical position and genetic distance will not working properly [optExcl] => * [optRequ] => --ped/--lgen [optWith] => * [detaildesc] => Proceed analyses regardless of presence of map file, variant name and position will be assigned arbitrary, so options related to chromosome, physical position and genetic distance will not working properly ) [makeclgeno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makeclgeno [longAname] => [shortAname] => [shortName] => -mz [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform genotype clumping based on the gene-variant mapping definition and export the clumped result [optExcl] => * [optRequ] => --qtest [optWith] => [detaildesc] => Perform genotype clumping based on the gene-variant mapping definition and export the clumped result ) [indel] => Array ( [is_given_default] => false [is_essential] => false [longName] => --indel [longAname] => [shortAname] => [shortName] => -ID [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Notify to WISARD that the input file have at least one indel variant. An error will be raised if --indel is not used for the dataset contains indel variant [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Notify to WISARD that the input file have at least one indel variant. An error will be raised if --indel is not used for the dataset contains indel variant ) [logistic] => Array ( [is_given_default] => false [is_essential] => false [longName] => --logistic [longAname] => [shortAname] => [shortName] => -lg [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Performs gene-level test after the fitting of logistic regression model under the assumption of unrelated dataset [optExcl] => * [optRequ] => --genetest [optWith] => [detaildesc] => Performs gene-level test after the fitting of logistic regression model under the assumption of unrelated dataset ) [sortvariant] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sortvariant [longAname] => [shortAname] => [shortName] => -sv [defVal] => asc [optType] => [optCat] => RT_OTHER [desc] => Sort the variants included in the final dataset with lexicographical order, if there is no additional parameter on this option, variants will be ordered by ascending order. Otherwise, it is possible to sort the variants by descending order by giving an additional parameter <b>desc</b> [optExcl] => --sortpos [optRequ] => * [optWith] => [detaildesc] => Sort the variants included in the final dataset with lexicographical order, if there is no additional parameter on this option, variants will be ordered by ascending order. Otherwise, it is possible to sort the variants by descending order by giving an additional parameter <b>desc</b> ) [sortpos] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sortpos [longAname] => [shortAname] => [shortName] => -sp [defVal] => asc [optType] => ascending order(asc) or descending order(desc) [optCat] => RT_OTHER [desc] => Sorting variants based on their physical position. This number [optExcl] => --sortvariant [optRequ] => * [optWith] => [detaildesc] => Sorting variants based on their physical position. This number ) [sortsample] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sortsample [longAname] => [shortAname] => [shortName] => -ss [defVal] => asc [optType] => ascending order(asc) or descending order(desc) [optCat] => RT_OTHER [desc] => Sort the samples included in the final dataset with lexicographical order by their FID and IID sequentially, if there is no additional parameter on this option, samples will be ordered by ascending order. Otherwise, it is possible to sort the samples by descending order by giving an additional parameter <b>desc</b> [optExcl] => --sortiid [optRequ] => * [optWith] => [detaildesc] => Sort the samples included in the final dataset with lexicographical order by their FID and IID sequentially, if there is no additional parameter on this option, samples will be ordered by ascending order. Otherwise, it is possible to sort the samples by descending order by giving an additional parameter <b>desc</b> ) [sortiid] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sortiid [longAname] => [shortAname] => [shortName] => -si [defVal] => asc [optType] => ascending order(asc) or descending order(desc) [optCat] => RT_OTHER [desc] => Sort the samples included in the final dataset with lexicographical order by their IID sequentially, if there is no additional parameter on this option, samples will be ordered by ascending order. Otherwise, it is possible to sort the samples by descending order by giving an additional parameter <b>desc</b> [optExcl] => --sortsample [optRequ] => * [optWith] => [detaildesc] => Sort the samples included in the final dataset with lexicographical order by their IID sequentially, if there is no additional parameter on this option, samples will be ordered by ascending order. Otherwise, it is possible to sort the samples by descending order by giving an additional parameter <b>desc</b> ) [baseline] => Array ( [is_given_default] => false [is_essential] => false [longName] => --baseline [longAname] => [shortAname] => [shortName] => -bl [defVal] => [optType] => string (comma[,] separated)<br />COLUMN=VALUE [optCat] => RT_OTHER [desc] => Set a baseline value of factor-type covariates, note that this assignment is only valid unless the type of assigned covariate is factor and the value should be exists in the "final" dataset, otherwise it will produce error [optExcl] => * [optRequ] => --sampvar,--cname,[FACTOR covariates] [optWith] => [detaildesc] => Set a baseline value of factor-type covariates, note that this assignment is only valid unless the type of assigned covariate is factor and the value should be exists in the "final" dataset, otherwise it will produce error ) [gz] => Array ( [is_given_default] => false [is_essential] => false [longName] => --gz [longAname] => [shortAname] => [shortName] => -Z [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Force gzipping to all outputs for reduced output size (only working under WISARD with gzip feature) [optExcl] => * [optRequ] => [WISARD with gzip] [optWith] => [detaildesc] => Force gzipping to all outputs for reduced output size (only working under WISARD with gzip feature) ) [ktau] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ktau [longAname] => [shortAname] => [shortName] => -kt [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Compute sample relatedness using Kendall's tau correlation coefficient, raw genotype used [optExcl] => --ibs,--corpearson,--cor,--kinship,--indep,--hybrid,--empktau,--empiall,--medcor [optRequ] => * [optWith] => [detaildesc] => Compute sample relatedness using Kendall's tau correlation coefficient, raw genotype used ) [empktau] => Array ( [is_given_default] => false [is_essential] => false [longName] => --empktau [longAname] => [shortAname] => [shortName] => -ek [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Compute sample relatedness using Kendall's tau correlation coefficient, normalized genotype used [optExcl] => --ibs,--corpearson,--cor,--kinship,--indep,--hybrid,--ktau,--empiall,--medcor [optRequ] => * [optWith] => [detaildesc] => Compute sample relatedness using Kendall's tau correlation coefficient, normalized genotype used ) [makenrm] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makenrm [longAname] => [shortAname] => [shortName] => -my [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export normalized genotype information [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export normalized genotype information ) [makeweight] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makeweight [longAname] => [shortAname] => [shortName] => -mw [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export computed/loaded weight values [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export computed/loaded weight values ) [nosampvarhdr] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nosampvarhdr [longAname] => [shortAname] => [shortName] => -nh [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Assume that there is NO header in the file assigned with --sampvar [optExcl] => * [optRequ] => --sampvar [optWith] => [detaildesc] => Assume that there is NO header in the file assigned with --sampvar ) [pvalrange] => Array ( [is_given_default] => false [is_essential] => false [longName] => --pvalrange [longAname] => [shortAname] => [shortName] => -pr [defVal] => [optType] => range (0~1) [optCat] => RT_01 [desc] => Export result only for those of p-values in the range [optExcl] => * [optRequ] => [Analyses producing p-value] [optWith] => [detaildesc] => Export result only for those of p-values in the range ) [time] => Array ( [is_given_default] => false [is_essential] => false [longName] => --time [longAname] => [shortAname] => [shortName] => -ti [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Report elapsed time for each result entry [optExcl] => * [optRequ] => [Analyses for multiple entries] [optWith] => [detaildesc] => Report elapsed time for each result entry ) [phenostdize] => Array ( [is_given_default] => false [is_essential] => false [longName] => --phenostdize [longAname] => [shortAname] => [shortName] => -pz [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Standardize given phenotype value, by standard deviation value from final phenotype after all adjustment [optExcl] => --invnorm [optRequ] => * [optWith] => [detaildesc] => Standardize given phenotype value, by standard deviation value from final phenotype after all adjustment ) [outmispheno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --outmispheno [longAname] => [shortAname] => [shortName] => -op [defVal] => -9 [optType] => string with no whitespace [optCat] => RT_OTHER [desc] => Assign the value for representing missing phenotype value when export final dataset [optExcl] => * [optRequ] => --makecov,--makeraw,--makeped,--makebed,--maketped,--makelgen,--makedom,--makerec,--makepheno [optWith] => [detaildesc] => Assign the value for representing missing phenotype value when export final dataset ) [outmisgeno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --outmisgeno [longAname] => [shortAname] => [shortName] => -og [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Missing string for genotypic NA when make output ) [gxecovs] => Array ( [is_given_default] => false [is_essential] => false [longName] => --gxecovs [longAname] => [shortAname] => [shortName] => -gc [defVal] => [optType] => string [optCat] => RT_OTHER [desc] => Determine the columns names to investigate GxE effect. Note that the columns included in here MUST BE a subset of --cname [optExcl] => * [optRequ] => --gxe [optWith] => [detaildesc] => Determine the columns names to investigate GxE effect. Note that the columns included in here MUST BE a subset of --cname ) [passemptyline] => Array ( [is_given_default] => false [is_essential] => false [longName] => --passemptyline [longAname] => [shortAname] => [shortName] => -pe [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Pass any empty line when retrieving ALL inputs [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Pass any empty line when retrieving ALL inputs ) [listvariant] => Array ( [is_given_default] => false [is_essential] => false [longName] => --listvariant [longAname] => [shortAname] => [shortName] => -lm [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export the list of variants in the final dataset [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export the list of variants in the final dataset ) [listsample] => Array ( [is_given_default] => false [is_essential] => false [longName] => --listsample [longAname] => [shortAname] => [shortName] => -ls [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export the list of samples in the final dataset [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export the list of samples in the final dataset ) [listfounder] => Array ( [is_given_default] => false [is_essential] => false [longName] => --listfounder [longAname] => [shortAname] => [shortName] => -lf [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export the list of founders in the final dataset [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export the list of founders in the final dataset ) [nolmm] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nolmm [longAname] => [shortAname] => [shortName] => -nl [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Never fit linear mixed model and assumes independency across variables in the model. This option affects all analyses using linear mixed model. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Never fit linear mixed model and assumes independency across variables in the model. This option affects all analyses using linear mixed model. ) [geneset] => Array ( [is_given_default] => false [is_essential] => false [longName] => --geneset [longAname] => [shortAname] => [shortName] => -pw [defVal] => [optType] => a file path of gene-set definition [optCat] => RT_OTHER [desc] => Retrieve gene-set definition from given path, and enables gene-set-testing mode. [optExcl] => * [optRequ] => --set [optWith] => [detaildesc] => Retrieve gene-set definition from given path, and enables gene-set-testing mode. ) [gsetconsec] => Array ( [is_given_default] => false [is_essential] => false [longName] => --gsetconsec [longAname] => [shortAname] => [shortName] => -GC [defVal] => [optType] => OT_RANGE [optCat] => RT_POS [desc] => Automatically generates gene-set definition by consecutive manner ) [nosysfeat] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nosysfeat [longAname] => [shortAname] => [shortName] => -ns [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Disable all system functinalities utilizing system-dependent spec. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Disable all system functinalities utilizing system-dependent spec. ) [fname] => Array ( [is_given_default] => false [is_essential] => false [longName] => --fname [longAname] => [shortAname] => [shortName] => -fc [defVal] => [optType] => Column of IDs to be factor covariate(s), divided by comma(,) w/o whitespace [optCat] => RT_OTHER [desc] => Assigns covariate(s) as factor-type. Unlike --cname, covariates in --fname <i>always</i> treated as factor type. [optExcl] => * [optRequ] => --sampvar [optWith] => [detaildesc] => Assigns covariate(s) as factor-type. Unlike --cname, covariates in --fname <i>always</i> treated as factor type. ) [makeev] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makeev [longAname] => [shortAname] => [shortName] => -mV [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export the result of eigendecomposition, consists of eigenvectors and eigenvalues. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export the result of eigendecomposition, consists of eigenvectors and eigenvalues. ) [ev] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ev [longAname] => [shortAname] => [shortName] => -ev [defVal] => [optType] => File path of pre-computed eigendecomposition, w/o extension [optCat] => RT_OTHER [desc] => Load pre-computed eigendecomposition, instead of compute it. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Load pre-computed eigendecomposition, instead of compute it. ) [natural] => Array ( [is_given_default] => false [is_essential] => false [longName] => --natural [longAname] => [shortAname] => [shortName] => -nt [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Apply <a href="http://www.codinghorror.com/blog/2007/12/sorting-for-humans-natural-sort-order.html">natural sort</a> when automatically sorting variants or samples. [optExcl] => * [optRequ] => --sortiid,--sortsample,--sortvariant [optWith] => [detaildesc] => Apply <a href="http://www.codinghorror.com/blog/2007/12/sorting-for-humans-natural-sort-order.html">natural sort</a> when automatically sorting variants or samples. ) [dupnaming] => Array ( [is_given_default] => false [is_essential] => false [longName] => --dupnaming [longAname] => [shortAname] => [shortName] => -dp [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => If some variant's name is duplicated, automatically correting the nume of sample. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => If some variant's name is duplicated, automatically correting the nume of sample. ) [acgt] => Array ( [is_given_default] => false [is_essential] => false [longName] => --acgt [longAname] => [shortAname] => [shortName] => -ac [defVal] => [optType] => Four characters corresponding to A, C, G, T, respectively [optCat] => RT_OTHER [desc] => Define the allele coding in the dataset corresponding to A, C, G and T, respectively. Note that the argument of this option must be four characters. [optExcl] => --1234,[non-ACGT dataset] [optRequ] => * [optWith] => [detaildesc] => Define the allele coding in the dataset corresponding to A, C, G and T, respectively. Note that the argument of this option must be four characters. ) [1234] => Array ( [is_given_default] => false [is_essential] => false [longName] => --1234 [longAname] => [shortAname] => [shortName] => -zz [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Assume that the genotype notation in the dataset file 1, 2, 3 and 4 are corresponding to actual genotype A, C, G and T, respectively. An error will be occurred if there is a character not 1, 2, 3, 4 nor missing genotype. [optExcl] => --acgt,[non-1234 dataset] [optRequ] => * [optWith] => [detaildesc] => Assume that the genotype notation in the dataset file 1, 2, 3 and 4 are corresponding to actual genotype A, C, G and T, respectively. An error will be occurred if there is a character not 1, 2, 3, 4 nor missing genotype. ) [sepallele] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sepallele [longAname] => [shortAname] => [shortName] => -sa [defVal] => [optType] => Single ascii character [optCat] => RT_OTHER [desc] => Define the separator of two alleles in the genotype data. A default separator is whitespace. [optExcl] => --consecallele [optRequ] => * [optWith] => [detaildesc] => Define the separator of two alleles in the genotype data. A default separator is whitespace. ) [consecallele] => Array ( [is_given_default] => false [is_essential] => false [longName] => --consecallele [longAname] => [shortAname] => [shortName] => -cl [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Assume that two alleles are consecutive when loading genotype data. [optExcl] => --sepallele [optRequ] => * [optWith] => [detaildesc] => Assume that two alleles are consecutive when loading genotype data. ) [citation] => Array ( [is_given_default] => false [is_essential] => false [longName] => --citation [longAname] => [shortAname] => [shortName] => -ce [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Print out the information for citation of this program and exit. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Print out the information for citation of this program and exit. ) [miss] => Array ( [is_given_default] => false [is_essential] => false [longName] => --miss [longAname] => [shortAname] => [shortName] => -mx [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Investigate genotype missingness against variant/sample/family and make report. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Investigate genotype missingness against variant/sample/family and make report. ) [misparent] => Array ( [is_given_default] => false [is_essential] => false [longName] => --misparent [longAname] => [shortAname] => [shortName] => -mq [defVal] => [optType] => String with no whitespace [optCat] => RT_OTHER [desc] => Determine character for the parental notation of founder. i.e., character for the parent is missing. [optExcl] => --noparent [optRequ] => * [optWith] => [detaildesc] => Determine character for the parental notation of founder. i.e., character for the parent is missing. ) [sampmajor] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sampmajor [longAname] => [shortAname] => [shortName] => -sm [defVal] => [optType] => [optCat] => RT_OTHER [desc] => Export PLINK BED file with sample-major format. [optExcl] => * [optRequ] => --makebed,--genesplit [optWith] => [detaildesc] => Export PLINK BED file with sample-major format. ) [nospecdcmp] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nospecdcmp [longAname] => [shortAname] => [shortName] => -ne [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Do not perform the spectral decomposition in any circumtances. [optExcl] => --specdcmp [optRequ] => * [optWith] => [detaildesc] => Do not perform the spectral decomposition in any circumtances. ) [species] => Array ( [is_given_default] => false [is_essential] => false [longName] => --species [longAname] => [shortAname] => [shortName] => -sc [defVal] => human [optType] => [optCat] => RT_OTHER [desc] => Set the species to be analyzed. To see the list of supported species, refer <a href='?act=dm_load#species'>this page</a> [detaildesc] => Set the species to be analyzed. To see the list of supported species, refer <a href='?act=dm_load#species'>this page</a> ) [nodata] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nodata [longAname] => [shortAname] => [shortName] => -nd [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Continus an execution although there is no genotype data. This option is required for some special analyses, which do not need any genotype data. [detaildesc] => Continus an execution although there is no genotype data. This option is required for some special analyses, which do not need any genotype data. ) [regex] => Array ( [is_given_default] => false [is_essential] => false [longName] => --regex [longAname] => [shortAname] => [shortName] => -er [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Use regular expression in the acceptable options ) [model] => Array ( [is_given_default] => true [is_essential] => false [longName] => --model [longAname] => [shortAname] => [shortName] => -J [defVal] => additive [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Genetic model used in the dataset ) [fqls] => Array ( [is_given_default] => false [is_essential] => false [longName] => --fqls [longAname] => [shortAname] => [shortName] => -qf [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform quasi-likelihood scoretest analyiss using pedigree structure [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform quasi-likelihood scoretest analyiss using pedigree structure ) [fqlsnopddt] => Array ( [is_given_default] => false [is_essential] => false [longName] => --fqlsnopddt [longAname] => [shortAname] => [shortName] => -pf [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => When perform Family QLS, do not force to use kinship coefficient when computing the offset of each sample. [optExcl] => * [optRequ] => --fqls,--mfqls [optWith] => [detaildesc] => When perform Family QLS, do not force to use kinship coefficient when computing the offset of each sample. ) [retestthr] => Array ( [is_given_default] => false [is_essential] => false [longName] => --retestthr [longAname] => [shortAname] => [shortName] => -rt [defVal] => 0.05 [optType] => real number (0~1) [optCat] => RT_01 [desc] => Set the p-value threshold to perform second-level unimputed FQLS when after imputed FQLS. Lesser number of variants will be incorporated as lesser this value [optExcl] => * [optRequ] => --fqls [optWith] => [detaildesc] => Set the p-value threshold to perform second-level unimputed FQLS when after imputed FQLS. Lesser number of variants will be incorporated as lesser this value ) [mqls] => Array ( [is_given_default] => false [is_essential] => false [longName] => --mqls [longAname] => [shortAname] => [shortName] => -qm [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform Modified QLStest. Note that MQLS will forcely disable genotype imputation when accompanied with --fqls so the analysis time will be long if there are missing genotypes [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform Modified QLStest. Note that MQLS will forcely disable genotype imputation when accompanied with --fqls so the analysis time will be long if there are missing genotypes ) [mfqls] => Array ( [is_given_default] => false [is_essential] => false [longName] => --mfqls [longAname] => [shortAname] => [shortName] => -qx [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform MFQLS test. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform MFQLS test. ) [avail] => Array ( [is_given_default] => false [is_essential] => false [longName] => --avail [longAname] => [shortAname] => [shortName] => -av [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform all analyses WITHOUT any imputation. If the analysis does not support a test without imputation, the result of that analysis for the makrer/gene having missing genotype will be NA [optExcl] => * [optRequ] => --fqls/--qls/--regression [optWith] => * [detaildesc] => Perform all analyses WITHOUT any imputation. If the analysis does not support a test without imputation, the result of that analysis for the makrer/gene having missing genotype will be NA ) [heri] => Array ( [is_given_default] => false [is_essential] => false [longName] => --heri [longAname] => [shortAname] => [shortName] => -hi [defVal] => 0 [optType] => real number (0~1) [optCat] => RT_OTHER [desc] => Assign the prior heritability for the analysis of expected power estimation [optExcl] => * [optRequ] => --powercalc [optWith] => * [detaildesc] => Assign the prior heritability for the analysis of expected power estimation ) [mqlsconsec] => Array ( [is_given_default] => false [is_essential] => false [longName] => --mqlsconsec [longAname] => [shortAname] => [shortName] => -qp [defVal] => [optType] => positive integer (>1) [optCat] => RT_POS [desc] => Perform MFQLS with given number of consecutive variants [optExcl] => * [optRequ] => --mqls [optWith] => [detaildesc] => Perform MFQLS with given number of consecutive variants ) [fastmqls] => Array ( [is_given_default] => false [is_essential] => false [longName] => --fastmqls [longAname] => [shortAname] => [shortName] => -Fa [defVal] => 0 [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Perform fast version of MQLS with genotype imputation ) [fastfqls] => Array ( [is_given_default] => false [is_essential] => false [longName] => --fastfqls [longAname] => [shortAname] => [shortName] => -FF [defVal] => 0 [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Perform fast version of FQLS with genotype imputation ) [genetest] => Array ( [is_given_default] => false [is_essential] => false [longName] => --genetest [longAname] => [shortAname] => [shortName] => -tg [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Perform basic two gene-level test (CMC and Collapsing method) [optExcl] => * [optRequ] => --set/--setconsec [optWith] => * [detaildesc] => Perform basic two gene-level test (CMC and Collapsing method) ) [genesummary] => Array ( [is_given_default] => false [is_essential] => false [longName] => --genesummary [longAname] => [shortAname] => [shortName] => -sg [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export brief summary for gene-variant corresponding result [optExcl] => * [optRequ] => --set/--setconsec [optWith] => * [detaildesc] => Export brief summary for gene-variant corresponding result ) [gmapsummary] => Array ( [is_given_default] => false [is_essential] => false [longName] => --gmapsummary [longAname] => [shortAname] => [shortName] => -xg [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export gene-variant mapping status. [optExcl] => * [optRequ] => --set [optWith] => [detaildesc] => Export gene-variant mapping status. ) [pedcmc] => Array ( [is_given_default] => false [is_essential] => false [longName] => --pedcmc [longAname] => [shortAname] => [shortName] => -pc [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform PedCMC test, in addition to --genetest [optExcl] => * [optRequ] => --genetest [optWith] => * [detaildesc] => Perform PedCMC test, in addition to --genetest ) [raremaf] => Array ( [is_given_default] => false [is_essential] => false [longName] => --raremaf [longAname] => [shortAname] => [shortName] => -rm [defVal] => 0.01 [optType] => real number (0~1) [optCat] => RT_01 [desc] => Set the MAF threshold divides rare/common of variant when doing --pedcmc [optExcl] => * [optRequ] => --pedcmc [optWith] => * [detaildesc] => Set the MAF threshold divides rare/common of variant when doing --pedcmc ) [genemiss] => Array ( [is_given_default] => false [is_essential] => false [longName] => --genemiss [longAname] => [shortAname] => [shortName] => -gm [defVal] => 0.05 [optType] => Real value ranged [0,1] [optCat] => RT_01 [desc] => Filtering genes by its genotyping rate from included variants [optExcl] => * [optRequ] => --set/--setconsec [optWith] => [detaildesc] => Filtering genes by its genotyping rate from included variants ) [genesize] => Array ( [is_given_default] => false [is_essential] => false [longName] => --genesize [longAname] => [shortAname] => [shortName] => -gr [defVal] => [optType] => range (positive integer) [optCat] => RT_NONNEG [desc] => Exclude all gene definitions do not satifies its number of variants included in gene definition [optExcl] => --setconsec [optRequ] => --set [optWith] => * [detaildesc] => Exclude all gene definitions do not satifies its number of variants included in gene definition ) [skato] => Array ( [is_given_default] => false [is_essential] => false [longName] => --skato [longAname] => [shortAname] => [shortName] => -so [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform SKAT-o test, in addition to --genetest [optExcl] => * [optRequ] => --genetest [optWith] => [detaildesc] => Perform SKAT-o test, in addition to --genetest ) [skat] => Array ( [is_given_default] => false [is_essential] => false [longName] => --skat [longAname] => [shortAname] => [shortName] => -sk [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform SKAT test, in addition to --genetest [optExcl] => * [optRequ] => --genetest [optWith] => [detaildesc] => Perform SKAT test, in addition to --genetest ) [skatondiv] => Array ( [is_given_default] => false [is_essential] => false [longName] => --skatondiv [longAname] => [shortAname] => [shortName] => -ov [defVal] => 0 [optType] => Positive integer (>=2) [optCat] => RT_POS [desc] => Set the number of division for the SKAT-o test.The size of each division is fixed to 1/(#division-2). [optExcl] => --skatodivs [optRequ] => --skato [optWith] => [detaildesc] => Set the number of division for the SKAT-o test.The size of each division is fixed to 1/(#division-2). ) [skatodivs] => Array ( [is_given_default] => false [is_essential] => false [longName] => --skatodivs [longAname] => [shortAname] => [shortName] => -oz [defVal] => [optType] => Values ranged [0,1], separated with comma(,) with no whitespace [optCat] => RT_OTHER [desc] => Set the user-defined rho values for SKAT-o computation. [optExcl] => --skatondiv [optRequ] => --skato [optWith] => [detaildesc] => Set the user-defined rho values for SKAT-o computation. ) [wsum] => Array ( [is_given_default] => false [is_essential] => false [longName] => --wsum [longAname] => [shortAname] => [shortName] => -ws [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform gene-level test using Weighted Sum statistic proposed by Madsen <i>et al.</i> [optExcl] => * [optRequ] => --genetest [optWith] => [detaildesc] => Perform gene-level test using Weighted Sum statistic proposed by Madsen <i>et al.</i> ) [kbac] => Array ( [is_given_default] => false [is_essential] => false [longName] => --kbac [longAname] => [shortAname] => [shortName] => -K [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform gene-level test using KBAC statistic proposed by Liu <i>et al.</i> [optExcl] => * [optRequ] => --genetest [optWith] => [detaildesc] => Perform gene-level test using KBAC statistic proposed by Liu <i>et al.</i> ) [kbacalpha] => Array ( [is_given_default] => false [is_essential] => false [longName] => --kbacalpha [longAname] => [shortAname] => [shortName] => -ka [defVal] => 0.05 [optType] => [optCat] => RT_01 [desc] => Setting alpha level of KBAC test [optExcl] => * [optRequ] => --kbac [optWith] => [detaildesc] => Setting alpha level of KBAC test ) [kbac2side] => Array ( [is_given_default] => false [is_essential] => false [longName] => --kbac2side [longAname] => [shortAname] => [shortName] => -k2 [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Performing 2-sided test and 1-sided test simultaneously in KBAC test. [optExcl] => * [optRequ] => --kbac [optWith] => [detaildesc] => Performing 2-sided test and 1-sided test simultaneously in KBAC test. ) [kbackernel] => Array ( [is_given_default] => false [is_essential] => false [longName] => --kbackernel [longAname] => [shortAname] => [shortName] => -kk [defVal] => hypergeometric [optType] => [optCat] => RT_OTHER [desc] => Change the kernel of KBAC test. [optExcl] => * [optRequ] => --kbac [optWith] => [detaildesc] => Change the kernel of KBAC test. ) [mfhom] => Array ( [is_given_default] => false [is_essential] => false [longName] => --mfhom [longAname] => [shortAname] => [shortName] => -mo [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform multi-FARVAT gene-level analysis under homogeneity assumption among phenotypes. [optExcl] => --mfhet,--longitudinal [optRequ] => --genetest,--set/--setconsec [optWith] => [detaildesc] => Perform multi-FARVAT gene-level analysis under homogeneity assumption among phenotypes. ) [mfhet] => Array ( [is_given_default] => false [is_essential] => false [longName] => --mfhet [longAname] => [shortAname] => [shortName] => -mf [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform multi-FARVAT gene-level analysis under heterogeneity assumption among phenotypes. [optExcl] => --hfhom,--longitudinal [optRequ] => --genetest,--set/--setconsec [optWith] => [detaildesc] => Perform multi-FARVAT gene-level analysis under heterogeneity assumption among phenotypes. ) [asum] => Array ( [is_given_default] => false [is_essential] => false [longName] => --asum [longAname] => [shortAname] => [shortName] => -au [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform adaptive-sum gene-level analysis [optExcl] => * [optRequ] => --genetest,--set/--setconsec [optWith] => [detaildesc] => Perform adaptive-sum gene-level analysis ) [makegeno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makegeno [longAname] => [shortAname] => [shortName] => -mZ [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Generate genotype file with RAW format, according to the definition of gene-variants mapping. [optExcl] => * [optRequ] => --set/--setconsec [optWith] => [detaildesc] => Generate genotype file with RAW format, according to the definition of gene-variants mapping. ) [farvat] => Array ( [is_given_default] => false [is_essential] => false [longName] => --farvat [longAname] => [shortAname] => [shortName] => -Fv [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform FARVAT analysis for gene-level association test. [optExcl] => * [optRequ] => --set/--setconsec [optWith] => [detaildesc] => Perform FARVAT analysis for gene-level association test. ) [pedgene] => Array ( [is_given_default] => false [is_essential] => false [longName] => --pedgene [longAname] => [shortAname] => [shortName] => -pg [defVal] => 0 [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Perform pedgene analysis ) [adjf1] => Array ( [is_given_default] => false [is_essential] => false [longName] => --adjf1 [longAname] => [shortAname] => [shortName] => -f1 [defVal] => 0 [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Adjust phenotype with FQLS method 1 ) [adjf2] => Array ( [is_given_default] => false [is_essential] => false [longName] => --adjf2 [longAname] => [shortAname] => [shortName] => -f2 [defVal] => 0 [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Adjust phenotype with FQLS method 2 ) [makefarvat] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makefarvat [longAname] => [shortAname] => [shortName] => -kf [defVal] => 0 [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Generate extra output of FARVAT for meta-analysis ) [farvatx] => Array ( [is_given_default] => false [is_essential] => false [longName] => --farvatx [longAname] => [shortAname] => [shortName] => -Fx [defVal] => 0 [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Perform FARVATX analysis ) [farvatxndiv] => Array ( [is_given_default] => false [is_essential] => false [longName] => --farvatxndiv [longAname] => [shortAname] => [shortName] => -Xv [defVal] => 5 [optType] => OT_NUMBER [optCat] => RT_POS [desc] => Number of divisions for FARVATX test ) [farvatxd] => Array ( [is_given_default] => false [is_essential] => false [longName] => --farvatxd [longAname] => [shortAname] => [shortName] => -Fd [defVal] => 0.5 [optType] => OT_REAL [optCat] => RT_01 [desc] => Assumed D in FARVATX analysis ) [qtest] => Array ( [is_given_default] => false [is_essential] => false [longName] => --qtest [longAname] => [shortAname] => [shortName] => -Q [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform Q-test analysis [optExcl] => * [optRequ] => --set/--setconsec [optWith] => * [detaildesc] => Perform Q-test analysis ) [qtestclump] => Array ( [is_given_default] => false [is_essential] => false [longName] => --qtestclump [longAname] => [shortAname] => [shortName] => -Qc [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Clumping highly-correlated variants into single column when performing Q-test [optExcl] => * [optRequ] => --qtest [optWith] => [detaildesc] => Clumping highly-correlated variants into single column when performing Q-test ) [qteststt] => Array ( [is_given_default] => false [is_essential] => false [longName] => --qteststt [longAname] => [shortAname] => [shortName] => -Qs [defVal] => 0.2 [optType] => range (0~1) [optCat] => RT_01 [desc] => Adjust soft truncation threshold for Q-test. [optExcl] => * [optRequ] => --qtest [optWith] => [detaildesc] => Adjust soft truncation threshold for Q-test. ) [qtestbetacov] => Array ( [is_given_default] => false [is_essential] => false [longName] => --qtestbetacov [longAname] => [shortAname] => [shortName] => -Qb [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export a variance-covariance of beta estimates for each gene-level test when perform Q-test. [optExcl] => * [optRequ] => --qtest [optWith] => [detaildesc] => Export a variance-covariance of beta estimates for each gene-level test when perform Q-test. ) [makebeta] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makebeta [longAname] => [shortAname] => [shortName] => -aa [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export beta estimates in Q-test [optExcl] => * [optRequ] => --qtest [optWith] => [detaildesc] => Export beta estimates in Q-test ) [mdr] => Array ( [is_given_default] => false [is_essential] => false [longName] => --mdr [longAname] => [shortAname] => [shortName] => -md [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform Multifactor Dimensionality Reductionanalysis [optExcl] => * [optRequ] => * [optWith] => --order,--top,--mdrthr,--cv,--loocv [detaildesc] => Perform Multifactor Dimensionality Reductionanalysis ) [order] => Array ( [is_given_default] => false [is_essential] => false [longName] => --order [longAname] => [shortAname] => [shortName] => -O [defVal] => 1 [optType] => positive integer [optCat] => RT_POS [desc] => Assigne the order of interaction in MDRanalysis [optExcl] => * [optRequ] => --mdr [optWith] => * [detaildesc] => Assigne the order of interaction in MDRanalysis ) [top] => Array ( [is_given_default] => false [is_essential] => false [longName] => --top [longAname] => [shortAname] => [shortName] => -T [defVal] => 1000 [optType] => positive integer [optCat] => RT_POS [desc] => Report top N results based on the balanced accuracy in MDRanalysis, rather than report all results [optExcl] => * [optRequ] => --mdr [optWith] => * [detaildesc] => Report top N results based on the balanced accuracy in MDRanalysis, rather than report all results ) [hmdr] => Array ( [is_given_default] => false [is_essential] => false [longName] => --hmdr [longAname] => [shortAname] => [shortName] => -hm [defVal] => [optType] => [optCat] => RT_POS [desc] => Perform Hierarchical MDRanalysis (unimplemented) [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Perform Hierarchical MDRanalysis (unimplemented) ) [hmdrall] => Array ( [is_given_default] => false [is_essential] => false [longName] => --hmdrall [longAname] => [shortAname] => [shortName] => -ha [defVal] => 1 [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Reports all possible HMDR results ) [hmdrprior] => Array ( [is_given_default] => false [is_essential] => false [longName] => --hmdrprior [longAname] => [shortAname] => [shortName] => -hp [defVal] => 1 [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Give priors to HMDR analysis ) [pharaoh] => Array ( [is_given_default] => false [is_essential] => false [longName] => --pharaoh [longAname] => [shortAname] => [shortName] => -gs [defVal] => 0 [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Perform PHARAOH analysis ) [proopt] => Array ( [is_given_default] => false [is_essential] => false [longName] => --proopt [longAname] => [shortAname] => [shortName] => -ho [defVal] => 0 [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Perform the detection of optimal lambda for PHARAOH only ) [prolambda] => Array ( [is_given_default] => false [is_essential] => false [longName] => --prolambda [longAname] => [shortAname] => [shortName] => -Pl [defVal] => 1000 [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Set the fixed lambda penalty for PHARAOH ) [prorange] => Array ( [is_given_default] => false [is_essential] => false [longName] => --prorange [longAname] => [shortAname] => [shortName] => -Pr [defVal] => [optType] => OT_RANGE [optCat] => RT_POS [desc] => Set the search range of optimal lambda ) [prothr] => Array ( [is_given_default] => false [is_essential] => false [longName] => --prothr [longAname] => [shortAname] => [shortName] => -Pt [defVal] => 0.0001 [optType] => OT_REAL [optCat] => RT_POS [desc] => Set the convergence threshold of finding optimal lambda ) [promaxiter] => Array ( [is_given_default] => false [is_essential] => false [longName] => --promaxiter [longAname] => [shortAname] => [shortName] => -gq [defVal] => 100 [optType] => OT_NUMBER [optCat] => RT_POS [desc] => Set the number of maximum iterations in PHARAOH ) [progenesize] => Array ( [is_given_default] => false [is_essential] => false [longName] => --progenesize [longAname] => [shortAname] => [shortName] => -Pg [defVal] => [optType] => OT_RANGE [optCat] => RT_NONNEG [desc] => Set the range of # variants in the gene to be included in the analysis ) [progsetsize] => Array ( [is_given_default] => false [is_essential] => false [longName] => --progsetsize [longAname] => [shortAname] => [shortName] => -pt [defVal] => [optType] => OT_RANGE [optCat] => RT_NONNEG [desc] => Set the range of # genes in the pathway to be included in the analysis ) [prosingle] => Array ( [is_given_default] => false [is_essential] => false [longName] => --prosingle [longAname] => [shortAname] => [shortName] => -Pe [defVal] => 0 [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Use a single penalty on PHARAOH analysis ) [propermcov] => Array ( [is_given_default] => false [is_essential] => false [longName] => --propermcov [longAname] => [shortAname] => [shortName] => -Pp [defVal] => 0 [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Permute covariates in PHARAOH ) [nperm] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nperm [longAname] => [shortAname] => [shortName] => -Ne [defVal] => 1000 [optType] => positive integer [optCat] => RT_POS [desc] => Set the number of permutations for the analyses using permutation scheme [optExcl] => * [optRequ] => --powercalc [optWith] => * [detaildesc] => Set the number of permutations for the analyses using permutation scheme ) [seqperm] => Array ( [is_given_default] => false [is_essential] => false [longName] => --seqperm [longAname] => [shortAname] => [shortName] => -SP [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Sequence of permutations to perform ) [permfile] => Array ( [is_given_default] => false [is_essential] => false [longName] => --permfile [longAname] => [shortAname] => [shortName] => -PF [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => User-defined permutations to perform, by sample IIDs ) [cv] => Array ( [is_given_default] => false [is_essential] => false [longName] => --cv [longAname] => [shortAname] => [shortName] => -cv [defVal] => [optType] => Positive integer > 1 [optCat] => RT_POS [desc] => Performs <i>k</i>-fold cross-validation in the analysis. [optExcl] => --loocv [optRequ] => --mdr [optWith] => * [detaildesc] => Performs <i>k</i>-fold cross-validation in the analysis. ) [gesca] => Array ( [is_given_default] => false [is_essential] => false [longName] => --gesca [longAname] => [shortAname] => [shortName] => -ge [defVal] => 0 [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Perform GeSCA ) [modeltype] => Array ( [is_given_default] => false [is_essential] => false [longName] => --modeltype [longAname] => [shortAname] => [shortName] => -MT [defVal] => formative [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Model type of GeSCA to perform (formative/reflective) ) [ggpath] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ggpath [longAname] => [shortAname] => [shortName] => -gp [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Gene-gene path data for pathway ) [makecolgeno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makecolgeno [longAname] => [shortAname] => [shortName] => -mO [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Export collapsed genotypes for each gene ) [debug] => Array ( [is_given_default] => false [is_essential] => false [longName] => --debug [longAname] => [shortAname] => [shortName] => -db [defVal] => 0 [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Run on debug mode ) [help] => Array ( [is_given_default] => false [is_essential] => false [longName] => --help [longAname] => [shortAname] => [shortName] => -hl [defVal] => 0 [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Print help ) [dosage] => Array ( [is_given_default] => false [is_essential] => false [longName] => --dosage [longAname] => [shortAname] => [shortName] => -d [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Assign input with dosage data, data type will be automatically determined. Full path of dosage data file with extension required [optExcl] => --vcf,--bcf,--ped,--tped,--bed,--simtrio,--lgen,--simfam [optRequ] => * [optWith] => [detaildesc] => Assign input with dosage data, data type will be automatically determined. Full path of dosage data file with extension required ) [expression] => Array ( [is_given_default] => false [is_essential] => false [longName] => --expression [longAname] => [shortAname] => [shortName] => -EX [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Expression input file prefix ) [vcf] => Array ( [is_given_default] => false [is_essential] => false [longName] => --vcf [longAname] => [shortAname] => [shortName] => -V [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Assign input with VCF file [optExcl] => --bcf,--tped,--ped,--dosage,--bed,--simtrio,--lgen,--simfam,--variantvar [optRequ] => * [optWith] => --filqual,--vcfqc [detaildesc] => Assign input with VCF file ) [simtrio] => Array ( [is_given_default] => false [is_essential] => false [longName] => --simtrio [longAname] => [shortAname] => [shortName] => -xt [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Alternate an input as simulated trio dataset, instead of external file [optExcl] => --tped,--ped,--dosage,--bed,--vcf,--lgen,--simfam [optRequ] => * [optWith] => [detaildesc] => Alternate an input as simulated trio dataset, instead of external file ) [nsim] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nsim [longAname] => [shortAname] => [shortName] => -sf [defVal] => 0 [optType] => OT_NUMBER [optCat] => RT_POS [desc] => Number of families in simulation ) [szvar] => Array ( [is_given_default] => false [is_essential] => false [longName] => --szvar [longAname] => [shortAname] => [shortName] => -z [defVal] => 0 [optType] => positive integer [optCat] => RT_POS [desc] => Set the number of variants simulated [optExcl] => * [optRequ] => --simfam [optWith] => [detaildesc] => Set the number of variants simulated ) [sim] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sim [longAname] => [shortAname] => [shortName] => -sF [defVal] => indep [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Use simulation dataset ) [trio] => Array ( [is_given_default] => false [is_essential] => false [longName] => --trio [longAname] => [shortAname] => [shortName] => -sT [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Let --simfam to generate trio-based family dataset. [optExcl] => * [optRequ] => --simfam [optWith] => [detaildesc] => Let --simfam to generate trio-based family dataset. ) [extfam] => Array ( [is_given_default] => false [is_essential] => false [longName] => --extfam [longAname] => [shortAname] => [shortName] => -sE [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Let --simfam to generate extended family dataset, that one family consists of ten members. [optExcl] => * [optRequ] => --simfam [optWith] => [detaildesc] => Let --simfam to generate extended family dataset, that one family consists of ten members. ) [nsig] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nsig [longAname] => [shortAname] => [shortName] => -nx [defVal] => 0 [optType] => positive integer [optCat] => RT_POS [desc] => While the generation of simulated data, set the number of 'statistically' significant variants. [optExcl] => * [optRequ] => --simfam [optWith] => [detaildesc] => While the generation of simulated data, set the number of 'statistically' significant variants. ) [sigmaf] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sigmaf [longAname] => [shortAname] => [shortName] => -XM [defVal] => 0.1 [optType] => OT_REAL [optCat] => RT_01 [desc] => Set MAF of simulation ) [simfreq] => Array ( [is_given_default] => false [is_essential] => false [longName] => --simfreq [longAname] => [shortAname] => [shortName] => -sq [defVal] => 0 [optType] => file path [optCat] => RT_OTHER [desc] => Use background MAF distribution to simulate dataset. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Use background MAF distribution to simulate dataset. ) [mafvar] => Array ( [is_given_default] => false [is_essential] => false [longName] => --mafvar [longAname] => [shortAname] => [shortName] => -ms [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Background MAF distribution file for the simulation of variants [optExcl] => * [optRequ] => --simfam/--simtrio [optWith] => [detaildesc] => Background MAF distribution file for the simulation of variants ) [pca] => Array ( [is_given_default] => false [is_essential] => false [longName] => --pca [longAname] => [shortAname] => [shortName] => -P [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform Principal Component Analysis (PCA) [optExcl] => * [optRequ] => * [optWith] => --npc,--proppc,--fullpca [detaildesc] => Perform Principal Component Analysis (PCA) ) [npc] => Array ( [is_given_default] => false [is_essential] => false [longName] => --npc [longAname] => [shortAname] => [shortName] => -N [defVal] => 5 [optType] => positive integer [optCat] => RT_POS [desc] => Determine the number of PCs computed. Note that this number cannot larger than the number of samples [optExcl] => --proppc,--fullpca [optRequ] => --pca [optWith] => * [detaildesc] => Determine the number of PCs computed. Note that this number cannot larger than the number of samples ) [proppc] => Array ( [is_given_default] => false [is_essential] => false [longName] => --proppc [longAname] => [shortAname] => [shortName] => -pp [defVal] => [optType] => Real value ranged (0,1] [optCat] => RT_01 [desc] => Extract an arbitrary number of PCs to explain given proportion of entire variance. [optExcl] => --npc,--fullpca [optRequ] => --pca [optWith] => [detaildesc] => Extract an arbitrary number of PCs to explain given proportion of entire variance. ) [usemf] => Array ( [is_given_default] => false [is_essential] => false [longName] => --usemf [longAname] => [shortAname] => [shortName] => -u [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Utilizing the missing founders in the analyses. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Utilizing the missing founders in the analyses. ) [fullpca] => Array ( [is_given_default] => false [is_essential] => false [longName] => --fullpca [longAname] => [shortAname] => [shortName] => -fu [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform full PCA with spectral decomposition. This option require much more time, but can compute all possible PCs [optExcl] => --npc,--proppc [optRequ] => --pca [optWith] => * [detaildesc] => Perform full PCA with spectral decomposition. This option require much more time, but can compute all possible PCs ) [rpath] => Array ( [is_given_default] => false [is_essential] => false [longName] => --rpath [longAname] => [shortAname] => [shortName] => -rl [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => (R-compatible version only) Assign the path for R initialization, in case of this option is not assigned, WISARD will automatically search the path [optExcl] => * [optRequ] => [WISARD with R] [optWith] => * [detaildesc] => (R-compatible version only) Assign the path for R initialization, in case of this option is not assigned, WISARD will automatically search the path ) [grm] => Array ( [is_given_default] => false [is_essential] => false [longName] => --grm [longAname] => [shortAname] => [shortName] => -gR [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Read the sample relatedness matrix computed from GCTA, and perform statistical analysis with the sample relatedness matrix computed from WISARD [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Read the sample relatedness matrix computed from GCTA, and perform statistical analysis with the sample relatedness matrix computed from WISARD ) [grmalpha] => Array ( [is_given_default] => false [is_essential] => false [longName] => --grmalpha [longAname] => [shortAname] => [shortName] => -ga [defVal] => 0.001 [optType] => real number(0~1) [optCat] => RT_01 [desc] => Set the alpha for confidence interval on the statistical analysis by --grm [optExcl] => * [optRequ] => --grm [optWith] => * [detaildesc] => Set the alpha for confidence interval on the statistical analysis by --grm ) [makeped] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makeped [longAname] => [shortAname] => [shortName] => -mp [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export final dataset as PED format [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Export final dataset as PED format ) [maketped] => Array ( [is_given_default] => false [is_essential] => false [longName] => --maketped [longAname] => [shortAname] => [shortName] => -mT [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export final dataset as transposed PED format [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Export final dataset as transposed PED format ) [makebed] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makebed [longAname] => [shortAname] => [shortName] => -mb [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export final dataset as BED format [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Export final dataset as BED format ) [makeraw] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makeraw [longAname] => [shortAname] => [shortName] => -mr [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export final dataset as RAW format [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Export final dataset as RAW format ) [makedom] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makedom [longAname] => [shortAname] => [shortName] => -mD [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export the final dataset as dominant coding [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export the final dataset as dominant coding ) [makerec] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makerec [longAname] => [shortAname] => [shortName] => -mR [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export the final dataset as recessive coding [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export the final dataset as recessive coding ) [makevcf] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makevcf [longAname] => [shortAname] => [shortName] => -mv [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Export final dataset as VCF format. Note that all genotypes in the dataset will be treated as unphased [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Export final dataset as VCF format. Note that all genotypes in the dataset will be treated as unphased ) [makebcf] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makebcf [longAname] => [shortAname] => [shortName] => -mF [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Generates dataset file with binary VCF format, using final dataset. [detaildesc] => Generates dataset file with binary VCF format, using final dataset. ) [makelgen] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makelgen [longAname] => [shortAname] => [shortName] => -mn [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export the final dataset as LGEN format [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Export the final dataset as LGEN format ) [makegen] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makegen [longAname] => [shortAname] => [shortName] => -mG [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export the final dataset as GEN format. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export the final dataset as GEN format. ) [makebgen] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makebgen [longAname] => [shortAname] => [shortName] => -mB [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export the final dataset as binary GEN format. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export the final dataset as binary GEN format. ) [makebeagle] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makebeagle [longAname] => [shortAname] => [shortName] => -mL [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Convert the final dataset to the format that can be accepted in Beagle program. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Convert the final dataset to the format that can be accepted in Beagle program. ) [makemdr] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makemdr [longAname] => [shortAname] => [shortName] => -mM [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Generates dataset file that can be accepted by MDR program, using final dataset. [detaildesc] => Generates dataset file that can be accepted by MDR program, using final dataset. ) [zipbgen] => Array ( [is_given_default] => false [is_essential] => false [longName] => --zipbgen [longAname] => [shortAname] => [shortName] => -zb [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Deflate the genotype probability data of binary GEN format. [optExcl] => * [optRequ] => --makebgen [optWith] => [detaildesc] => Deflate the genotype probability data of binary GEN format. ) [filqual] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filqual [longAname] => [shortAname] => [shortName] => -fq [defVal] => [optType] => Positive integer [optCat] => RT_NONNEG [desc] => Filtering variants having its QUAL value in VCF within specific range. [optExcl] => --incqual [optRequ] => --vcf/--bcf [optWith] => --window [detaildesc] => Filtering variants having its QUAL value in VCF within specific range. ) [incqual] => Array ( [is_given_default] => false [is_essential] => false [longName] => --incqual [longAname] => [shortAname] => [shortName] => -iq [defVal] => [optType] => Positive integer [optCat] => RT_NONNEG [desc] => Selecting variants having its QUAL value in VCF within specific range. [optExcl] => --filqual [optRequ] => --vcf [optWith] => * [detaildesc] => Selecting variants having its QUAL value in VCF within specific range. ) [mendel] => Array ( [is_given_default] => false [is_essential] => false [longName] => --mendel [longAname] => [shortAname] => [shortName] => -m [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Perform the integrity of Mendel inheritance across families. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform the integrity of Mendel inheritance across families. ) [filmendelfam] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filmendelfam [longAname] => [shortAname] => [shortName] => -rF [defVal] => [optType] => Family IDs divided by comma(,) w/o whitespace or file path [optCat] => RT_01 [desc] => Filtering samples having their family-level Mendelian error rate is within specific range. [optExcl] => --incmendelfam [optRequ] => * [optWith] => [detaildesc] => Filtering samples having their family-level Mendelian error rate is within specific range. ) [incmendelfam] => Array ( [is_given_default] => false [is_essential] => false [longName] => --incmendelfam [longAname] => [shortAname] => [shortName] => -xF [defVal] => [optType] => Family IDs divided by comma(,) w/o whitespace or file path [optCat] => RT_01 [desc] => Including samples having their family-level Mendelian error rate is within specific range. [optExcl] => --filmendelfam [optRequ] => * [optWith] => [detaildesc] => Including samples having their family-level Mendelian error rate is within specific range. ) [filmendelsamp] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filmendelsamp [longAname] => [shortAname] => [shortName] => -rS [defVal] => [optType] => Individual IDs divided by comma(,) w/o whitespace or file path [optCat] => RT_01 [desc] => Filtering samples having its Mendelian error rate is within specific range. [optExcl] => --incmendelsamp [optRequ] => * [optWith] => [detaildesc] => Filtering samples having its Mendelian error rate is within specific range. ) [incmendelsamp] => Array ( [is_given_default] => false [is_essential] => false [longName] => --incmendelsamp [longAname] => [shortAname] => [shortName] => -xS [defVal] => [optType] => Individual IDs divided by comma(,) w/o whitespace or file path [optCat] => RT_01 [desc] => Including samples having its Mendelian error rate is within specific range. [optExcl] => --filmendelsamp [optRequ] => * [optWith] => [detaildesc] => Including samples having its Mendelian error rate is within specific range. ) [filmendelvar] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filmendelvar [longAname] => [shortAname] => [shortName] => -ds [defVal] => [optType] => Variant identifiers divided by comma(,) w/o whitespace or file path [optCat] => RT_01 [desc] => Filtering variants having its Mendelian error rate is within specific range. [optExcl] => --incmendelvar [optRequ] => * [optWith] => [detaildesc] => Filtering variants having its Mendelian error rate is within specific range. ) [incmendelvar] => Array ( [is_given_default] => false [is_essential] => false [longName] => --incmendelvar [longAname] => [shortAname] => [shortName] => -xm [defVal] => [optType] => Variant identifiers divided by comma(,) w/o whitespace or file path [optCat] => RT_01 [desc] => Including variants having its Mendelian error rate is within specific range. [optExcl] => --filmendelvar [optRequ] => * [optWith] => [detaildesc] => Including variants having its Mendelian error rate is within specific range. ) [lrt] => Array ( [is_given_default] => false [is_essential] => false [longName] => --lrt [longAname] => [shortAname] => [shortName] => -lr [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform LRT test based on variant-wise model additional to the score test (it will takes much time) [optExcl] => * [optRequ] => --scoretest [optWith] => * [detaildesc] => Perform LRT test based on variant-wise model additional to the score test (it will takes much time) ) [vcfqc] => Array ( [is_given_default] => false [is_essential] => false [longName] => --vcfqc [longAname] => [shortAname] => [shortName] => -vq [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Retrieve only the makers having its variant quality is PASS when process VCF input [optExcl] => * [optRequ] => --vcf/--bcf [optWith] => * [detaildesc] => Retrieve only the makers having its variant quality is PASS when process VCF input ) [phasedonly] => Array ( [is_given_default] => false [is_essential] => false [longName] => --phasedonly [longAname] => [shortAname] => [shortName] => -po [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => In the loading of VCF file, remove out all genotypes except fo properly phased genotype. [optExcl] => --unphasedonly [optRequ] => --vcf [optWith] => [detaildesc] => In the loading of VCF file, remove out all genotypes except fo properly phased genotype. ) [unphasedonly] => Array ( [is_given_default] => false [is_essential] => false [longName] => --unphasedonly [longAname] => [shortAname] => [shortName] => -uo [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => In the loading of VCF file, remove out all genotypes except fo properly unphased genotype. [optExcl] => --phasedonly [optRequ] => --vcf [optWith] => [detaildesc] => In the loading of VCF file, remove out all genotypes except fo properly unphased genotype. ) [interactive] => Array ( [is_given_default] => false [is_essential] => false [longName] => --interactive [longAname] => [shortAname] => [shortName] => -I [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Run WISARD as an interactive execution mode. Note that the arguments assigned with this option will affect [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Run WISARD as an interactive execution mode. Note that the arguments assigned with this option will affect ) [qls] => Array ( [is_given_default] => false [is_essential] => false [longName] => --qls [longAname] => [shortAname] => [shortName] => -ql [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform quasi-likelihood scoretest analysis [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform quasi-likelihood scoretest analysis ) [regression] => Array ( [is_given_default] => false [is_essential] => false [longName] => --regression [longAname] => [shortAname] => [shortName] => -rg [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform variant-wise regression analysis. Linear or logistic regression will be selected according to phenotype [optExcl] => * [optRequ] => * [optWith] => --gxe,--avail,--sampvar,--pname,--cname,--pc2cov [detaildesc] => Perform variant-wise regression analysis. Linear or logistic regression will be selected according to phenotype ) [check] => Array ( [is_given_default] => false [is_essential] => false [longName] => --check [longAname] => [shortAname] => [shortName] => -ck [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Check system, not available in public version. [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Check system, not available in public version. ) [gxe] => Array ( [is_given_default] => false [is_essential] => false [longName] => --gxe [longAname] => [shortAname] => [shortName] => -gx [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => In the regression analysis, include additional covariates that regarding an interaction between genotype and given covariates [optExcl] => * [optRequ] => --regression [optWith] => * [detaildesc] => In the regression analysis, include additional covariates that regarding an interaction between genotype and given covariates ) [beta] => Array ( [is_given_default] => false [is_essential] => false [longName] => --beta [longAname] => [shortAname] => [shortName] => -be [defVal] => 0 [optType] => real number [optCat] => RT_NUM [desc] => Assign the effect of case-control differenc(beta) for the analysis of expected power estimation [optExcl] => * [optRequ] => --powercalc [optWith] => * [detaildesc] => Assign the effect of case-control differenc(beta) for the analysis of expected power estimation ) [rho] => Array ( [is_given_default] => false [is_essential] => false [longName] => --rho [longAname] => [shortAname] => [shortName] => -rh [defVal] => 0 [optType] => real number (-1~1) [optCat] => RT_ABS1 [desc] => Assign the prior correlation for the analysis of expected power estimation [optExcl] => * [optRequ] => --powercalc [optWith] => * [detaildesc] => Assign the prior correlation for the analysis of expected power estimation ) [rhopheno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --rhopheno [longAname] => [shortAname] => [shortName] => -rp [defVal] => 0 [optType] => real number (-1~1) [optCat] => RT_ABS1 [desc] => Assign the prior correlation among phenotypes for the analysis of expected power estimation [optExcl] => * [optRequ] => --powercalc [optWith] => * [detaildesc] => Assign the prior correlation among phenotypes for the analysis of expected power estimation ) [nsamp] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nsamp [longAname] => [shortAname] => [shortName] => -Ns [defVal] => 0 [optType] => positive integer [optCat] => RT_POS [desc] => Assign the number of samples for the analysis of expected power estimation [optExcl] => * [optRequ] => --powercalc [optWith] => * [detaildesc] => Assign the number of samples for the analysis of expected power estimation ) [npheno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --npheno [longAname] => [shortAname] => [shortName] => -Np [defVal] => 0 [optType] => positive integer [optCat] => RT_POS [desc] => Assign the number phenotypes for the analysis of expected power estimation [optExcl] => * [optRequ] => --powercalc [optWith] => * [detaildesc] => Assign the number phenotypes for the analysis of expected power estimation ) [noshuffle] => Array ( [is_given_default] => false [is_essential] => false [longName] => --noshuffle [longAname] => [shortAname] => [shortName] => -Nh [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => (For validation purpose) Do not shuffle the phenotype information when perform expected power estimation analysis [optExcl] => * [optRequ] => --powercalc [optWith] => * [detaildesc] => (For validation purpose) Do not shuffle the phenotype information when perform expected power estimation analysis ) [shuffle] => Array ( [is_given_default] => false [is_essential] => false [longName] => --shuffle [longAname] => [shortAname] => [shortName] => -sh [defVal] => 0 [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Shuffle case/control split in MDR analysis for train/test scheme ) [powercalc] => Array ( [is_given_default] => false [is_essential] => false [longName] => --powercalc [longAname] => [shortAname] => [shortName] => -pl [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform the analysis of expected statistical power under given conditions [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Perform the analysis of expected statistical power under given conditions ) [powercalc2] => Array ( [is_given_default] => false [is_essential] => false [longName] => --powercalc2 [longAname] => [shortAname] => [shortName] => -px [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform the analysis of expected statistical power under given conditions [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform the analysis of expected statistical power under given conditions ) [split] => Array ( [is_given_default] => false [is_essential] => false [longName] => --split [longAname] => [shortAname] => [shortName] => -sl [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Split input dataset along with the chromosomes. Note that the variants within unmapped chromosomes will be [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Split input dataset along with the chromosomes. Note that the variants within unmapped chromosomes will be ) [merge] => Array ( [is_given_default] => false [is_essential] => false [longName] => --merge [longAname] => [shortAname] => [shortName] => -me [defVal] => [optType] => Set of files divided by comma(,) w/o whitespace or file path [optCat] => RT_OTHER [desc] => From the 'base' dataset, load files from argument or path and merge all of them. [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => From the 'base' dataset, load files from argument or path and merge all of them. ) [mergemode] => Array ( [is_given_default] => false [is_essential] => false [longName] => --mergemode [longAname] => [shortAname] => [shortName] => -mm [defVal] => 1 [optType] => One of 1,2,3,4,5 [optCat] => RT_NONNEG [desc] => Set the proper merging strategy for the two genotyping having same variant name and its position. [optExcl] => * [optRequ] => --merge [optWith] => [detaildesc] => Set the proper merging strategy for the two genotyping having same variant name and its position. ) [testmatrix] => Array ( [is_given_default] => false [is_essential] => false [longName] => --testmatrix [longAname] => [shortAname] => [shortName] => -Xm [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform the exhaustive testing for matrix-related problem. [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Perform the exhaustive testing for matrix-related problem. ) [testmatfunc] => Array ( [is_given_default] => false [is_essential] => false [longName] => --testmatfunc [longAname] => [shortAname] => [shortName] => -Xt [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform the test for matrix functionality, not available in public version. [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Perform the test for matrix functionality, not available in public version. ) [testmatclass] => Array ( [is_given_default] => false [is_essential] => false [longName] => --testmatclass [longAname] => [shortAname] => [shortName] => -Xc [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform the test for matrix class, not available in public version. [optExcl] => * [optRequ] => * [optWith] => * [detaildesc] => Perform the test for matrix class, not available in public version. ) [testfunc] => Array ( [is_given_default] => false [is_essential] => false [longName] => --testfunc [longAname] => [shortAname] => [shortName] => -Xf [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform the test for functionality, not available in public version. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform the test for functionality, not available in public version. ) [longitudinal] => Array ( [is_given_default] => false [is_essential] => false [longName] => --longitudinal [longAname] => [shortAname] => [shortName] => -L [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Perform gene-level test based against longitudinal phenotype [optExcl] => --mfhom,--mfhet [optRequ] => --genetest,--sampvar,--pname,--set/--setconsec [optWith] => [detaildesc] => Perform gene-level test based against longitudinal phenotype ) [vt] => Array ( [is_given_default] => false [is_essential] => false [longName] => --vt [longAname] => [shortAname] => [shortName] => -vt [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform Variable-Threshold test [optExcl] => * [optRequ] => --genetest [optWith] => [detaildesc] => Perform Variable-Threshold test ) [famvt] => Array ( [is_given_default] => false [is_essential] => false [longName] => --famvt [longAname] => [shortAname] => [shortName] => -fv [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform Variable Threshold gene-level test for family dataset. [optExcl] => * [optRequ] => --genetest,--set/--setconsec [optWith] => [detaildesc] => Perform Variable Threshold gene-level test for family dataset. ) [ld] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ld [longAname] => [shortAname] => [shortName] => -ld [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Perform pair-wise LD computation with given conditions, exhaustive pair LD will be computed unless no further condition is assigned [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform pair-wise LD computation with given conditions, exhaustive pair LD will be computed unless no further condition is assigned ) [ldcor] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ldcor [longAname] => [shortAname] => [shortName] => -lc [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Compute LD based on Pearson's correlation coefficient. [optExcl] => * [optRequ] => --ld [optWith] => [detaildesc] => Compute LD based on Pearson's correlation coefficient. ) [annogene] => Array ( [is_given_default] => false [is_essential] => false [longName] => --annogene [longAname] => [shortAname] => [shortName] => -ag [defVal] => [optType] => A path of annotation file [optCat] => RT_OTHER [desc] => Assign the annotation of variants to WISARD and annotate variants. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Assign the annotation of variants to WISARD and annotate variants. ) [annorange] => Array ( [is_given_default] => false [is_essential] => false [longName] => --annorange [longAname] => [shortAname] => [shortName] => -ar [defVal] => 0 [optType] => Positive integer [optCat] => RT_POS [desc] => Set the range of annotation based on the proximity of variant to the adjacent genes. [optExcl] => * [optRequ] => --annogene [optWith] => [detaildesc] => Set the range of annotation based on the proximity of variant to the adjacent genes. ) [annovar] => Array ( [is_given_default] => false [is_essential] => false [longName] => --annovar [longAname] => [shortAname] => [shortName] => -as [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Annotate variant information to result [optExcl] => * [optRequ] => * [optWith] => ) [gemma] => Array ( [is_given_default] => false [is_essential] => false [longName] => --gemma [longAname] => [shortAname] => [shortName] => -G [defVal] => 0 [optType] => [optCat] => RT_ONOFF [desc] => Performs GEMMA [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Performs GEMMA ) [density] => Array ( [is_given_default] => false [is_essential] => false [longName] => --density [longAname] => [shortAname] => [shortName] => -de [defVal] => 0 [optType] => [optCat] => RT_POS [desc] => Investigate the density of variants based on their physical positions on the chromosome and make a histogram-like report [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Investigate the density of variants based on their physical positions on the chromosome and make a histogram-like report ) [tstv] => Array ( [is_given_default] => false [is_essential] => false [longName] => --tstv [longAname] => [shortAname] => [shortName] => -tt [defVal] => 0 [optType] => [optCat] => RT_POS [desc] => Investigate ts/tv ratio of the variants by the window that based on their physical positions on the chromosome and make a report for them [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Investigate ts/tv ratio of the variants by the window that based on their physical positions on the chromosome and make a report for them ) [sep] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sep [longAname] => [shortAname] => [shortName] => -xp [defVal] => [optType] => Single ascii character [optCat] => RT_OTHER [desc] => Set the field separator for the loading of dosage file [optExcl] => * [optRequ] => ??? [optWith] => [detaildesc] => Set the field separator for the loading of dosage file ) [dsgdist] => Array ( [is_given_default] => false [is_essential] => false [longName] => --dsgdist [longAname] => [shortAname] => [shortName] => -dd [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export dosage distribution [optExcl] => * [optRequ] => --dosage [optWith] => [detaildesc] => Export dosage distribution ) [pc2cov] => Array ( [is_given_default] => false [is_essential] => false [longName] => --pc2cov [longAname] => [shortAname] => [shortName] => -p2 [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Incorporate computed PCs as covariates [optExcl] => * [optRequ] => --pca [optWith] => [detaildesc] => Incorporate computed PCs as covariates ) [donull] => Array ( [is_given_default] => false [is_essential] => false [longName] => --donull [longAname] => [shortAname] => [shortName] => -dn [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => When performing regression analysis with --regression, fit null model and export its results. [optExcl] => * [optRequ] => --regression [optWith] => [detaildesc] => When performing regression analysis with --regression, fit null model and export its results. ) [explore] => Array ( [is_given_default] => false [is_essential] => false [longName] => --explore [longAname] => [shortAname] => [shortName] => -e [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Launch interactive shell for exploration of final dataset [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Launch interactive shell for exploration of final dataset ) [updvariant] => Array ( [is_given_default] => false [is_essential] => false [longName] => --updvariant [longAname] => [shortAname] => [shortName] => -um [defVal] => [optType] => a file path consisting 4 columns [optCat] => RT_OTHER [desc] => Update the entire variant table by currently inserted dataset. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Update the entire variant table by currently inserted dataset. ) [updchr] => Array ( [is_given_default] => false [is_essential] => false [longName] => --updchr [longAname] => [shortAname] => [shortName] => -uc [defVal] => * [optType] => A file path of variants and its chromosome to be updated [optCat] => RT_OTHER [desc] => Update the chromosome of corresponding variant between original dataset and name-changing table file. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Update the chromosome of corresponding variant between original dataset and name-changing table file. ) [updname] => Array ( [is_given_default] => false [is_essential] => false [longName] => --updname [longAname] => [shortAname] => [shortName] => -un [defVal] => * [optType] => A file path of variants and its new name to be updated [optCat] => RT_OTHER [desc] => Update the variant's name of corresponding variant between original dataset and name-changing table file. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Update the variant's name of corresponding variant between original dataset and name-changing table file. ) [updgdist] => Array ( [is_given_default] => false [is_essential] => false [longName] => --updgdist [longAname] => [shortAname] => [shortName] => -ud [defVal] => * [optType] => A file path of variants and new genetic distance to be updated [optCat] => RT_OTHER [desc] => Update the genetic distance of corresponding variant between original dataset and name-changing table file. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Update the genetic distance of corresponding variant between original dataset and name-changing table file. ) [updpos] => Array ( [is_given_default] => false [is_essential] => false [longName] => --updpos [longAname] => [shortAname] => [shortName] => -up [defVal] => * [optType] => A file path of variants and new position to be updated [optCat] => RT_OTHER [desc] => Update the actual position of corresponding variant between original dataset and name-changing table file. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Update the actual position of corresponding variant between original dataset and name-changing table file. ) [updgeno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --updgeno [longAname] => [shortAname] => [shortName] => -ug [defVal] => [optType] => A file path of genotypes to alter current dataset [optCat] => RT_OTHER [desc] => Update the entire genotype by input matrix. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Update the entire genotype by input matrix. ) [ref] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ref [longAname] => [shortAname] => [shortName] => -rf [defVal] => [optType] => A path of reference FASTA sequence [optCat] => RT_OTHER [desc] => Assign the reference FASTA sequence to WISARD [optExcl] => * [optRequ] => --makevcf [optWith] => [detaildesc] => Assign the reference FASTA sequence to WISARD ) [tdt] => Array ( [is_given_default] => false [is_essential] => false [longName] => --tdt [longAname] => [shortAname] => [shortName] => -td [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Perform Transmission Disequilibrium Test (TDT). Note that this test requires pedigree information. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform Transmission Disequilibrium Test (TDT). Note that this test requires pedigree information. ) [sdt] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sdt [longAname] => [shortAname] => [shortName] => -st [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Perform Sibship Disequilibrium Test (SDT). Note that this test requires pedigree information and multiple siblings for each family. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform Sibship Disequilibrium Test (SDT). Note that this test requires pedigree information and multiple siblings for each family. ) [ldbin] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ldbin [longAname] => [shortAname] => [shortName] => -lb [defVal] => 0 [optType] => [optCat] => RT_POS [desc] => Constraints LD computation to make pair for only N adjacent variants. Adjacency will be determined with chromosome and position [optExcl] => --ldsize [optRequ] => --ld [optWith] => [detaildesc] => Constraints LD computation to make pair for only N adjacent variants. Adjacency will be determined with chromosome and position ) [ldsize] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ldsize [longAname] => [shortAname] => [shortName] => -lS [defVal] => 0 [optType] => Positive integer [optCat] => RT_POS [desc] => Constraints LD computation to make pair for the variants within specified range. Adjacency will be determined with chromosome and position [optExcl] => --ldbin [optRequ] => --ld [optWith] => [detaildesc] => Constraints LD computation to make pair for the variants within specified range. Adjacency will be determined with chromosome and position ) [ldvar] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ldvar [longAname] => [shortAname] => [shortName] => -lM [defVal] => [optType] => Variant identifiers divided by comma(,) w/o whitespace or file path [optCat] => RT_OTHER [desc] => Determine the variant to investigate exhaustive two-way LD. [optExcl] => * [optRequ] => --ld [optWith] => [detaildesc] => Determine the variant to investigate exhaustive two-way LD. ) [remna] => Array ( [is_given_default] => false [is_essential] => false [longName] => --remna [longAname] => [shortAname] => [shortName] => -rn [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => From all results, remove the all NA's for main-term evaluation. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => From all results, remove the all NA's for main-term evaluation. ) [boost] => Array ( [is_given_default] => false [is_essential] => false [longName] => --boost [longAname] => [shortAname] => [shortName] => -bo [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Perform BOOST analysis for quickly finding Gene-Gene interaction. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform BOOST analysis for quickly finding Gene-Gene interaction. ) [thrboost] => Array ( [is_given_default] => false [is_essential] => false [longName] => --thrboost [longAname] => [shortAname] => [shortName] => -Bt [defVal] => 30 [optType] => Positive real number [optCat] => RT_NONNEG [desc] => Determine the reporting threshold for BOOST analysis. [optExcl] => * [optRequ] => --boost [optWith] => [detaildesc] => Determine the reporting threshold for BOOST analysis. ) [quickepi] => Array ( [is_given_default] => false [is_essential] => false [longName] => --quickepi [longAname] => [shortAname] => [shortName] => -qe [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Perform the fast-epistasis analysis proposed in PLINK [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform the fast-epistasis analysis proposed in PLINK ) [ext] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ext [longAname] => [shortAname] => [shortName] => -X [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Load external libraries for WISARD and execute them. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Load external libraries for WISARD and execute them. ) [gmdr] => Array ( [is_given_default] => false [is_essential] => false [longName] => --gmdr [longAname] => [shortAname] => [shortName] => -gd [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Perform Generalized MDR analysis for quickly finding Gene-Gene interaction for continuous phenotype. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform Generalized MDR analysis for quickly finding Gene-Gene interaction for continuous phenotype. ) [impute] => Array ( [is_given_default] => false [is_essential] => false [longName] => --impute [longAname] => [shortAname] => [shortName] => -ie [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Impute entire dataset according to the pedigree structure of given dataset. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Impute entire dataset according to the pedigree structure of given dataset. ) [lod] => Array ( [is_given_default] => false [is_essential] => false [longName] => --lod [longAname] => [shortAname] => [shortName] => -lo [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Perform LoD analysis [optExcl] => * [optRequ] => * [optWith] => ) [makeimpute] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makeimpute [longAname] => [shortAname] => [shortName] => -mi [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export imputed dataset [optExcl] => * [optRequ] => --impute [optWith] => [detaildesc] => Export imputed dataset ) [sxa] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sxa [longAname] => [shortAname] => [shortName] => -xa [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Perform sample selection analysis from given pedigree structure. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform sample selection analysis from given pedigree structure. ) [R] => Array ( [is_given_default] => false [is_essential] => false [longName] => --R [longAname] => [shortAname] => [shortName] => -R [defVal] => [optType] => [optCat] => RT_OTHER [desc] => When WISARD supports R connectivity, execute user-defined R code for the customized analysis. If multiple files assigned, it will be executed sequentially. [optExcl] => * [optRequ] => R connectivity [optWith] => [detaildesc] => When WISARD supports R connectivity, execute user-defined R code for the customized analysis. If multiple files assigned, it will be executed sequentially. ) [randbinpheno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --randbinpheno [longAname] => [shortAname] => [shortName] => -rb [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Generate random dichotomous phenotype and alternate if there is phenotype. [optExcl] => --randpheno [optRequ] => * [optWith] => [detaildesc] => Generate random dichotomous phenotype and alternate if there is phenotype. ) [randpheno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --randpheno [longAname] => [shortAname] => [shortName] => -re [defVal] => 1 [optType] => [optCat] => RT_POS [desc] => Generate random continuous phenotype based on the standard normal distribution, and alternate if there is phenotype. [optExcl] => --randbinpheno [optRequ] => * [optWith] => [detaildesc] => Generate random continuous phenotype based on the standard normal distribution, and alternate if there is phenotype. ) [genoctrl] => Array ( [is_given_default] => false [is_essential] => false [longName] => --genoctrl [longAname] => [shortAname] => [shortName] => -gl [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Use genomic control method to adjust p-values when performing multiple testing correction. [optExcl] => * [optRequ] => --adjust [optWith] => [detaildesc] => Use genomic control method to adjust p-values when performing multiple testing correction. ) [usergc] => Array ( [is_given_default] => false [is_essential] => false [longName] => --usergc [longAname] => [shortAname] => [shortName] => -eg [defVal] => [optType] => Positive real number [optCat] => RT_POS [desc] => When applying multiple testing correction to the analysis, assign user-defined Genomic control value instead of compute it from given statistics. [optExcl] => * [optRequ] => --adjust [optWith] => [detaildesc] => When applying multiple testing correction to the analysis, assign user-defined Genomic control value instead of compute it from given statistics. ) [adjust] => Array ( [is_given_default] => false [is_essential] => false [longName] => --adjust [longAname] => [shortAname] => [shortName] => -A [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Apply multiple testing corretion method to the result, and produce extra result. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Apply multiple testing corretion method to the result, and produce extra result. ) [famuniq] => Array ( [is_given_default] => false [is_essential] => false [longName] => --famuniq [longAname] => [shortAname] => [shortName] => -fU [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export the list of variants having its minor allele only for specific family, not the other family. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export the list of variants having its minor allele only for specific family, not the other family. ) [popuniq] => Array ( [is_given_default] => false [is_essential] => false [longName] => --popuniq [longAname] => [shortAname] => [shortName] => -pU [defVal] => [optType] => [optCat] => RT_OTHER [desc] => Based on the population definition, reports the list of population-specific variants. [detaildesc] => Based on the population definition, reports the list of population-specific variants. ) [monotone] => Array ( [is_given_default] => false [is_essential] => false [longName] => --monotone [longAname] => [shortAname] => [shortName] => -tm [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export the list of variants having no minor allele. Note that the definition of 'having no minor allele' might be depends on the dataset or filters applied. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export the list of variants having no minor allele. Note that the definition of 'having no minor allele' might be depends on the dataset or filters applied. ) [singleton] => Array ( [is_given_default] => false [is_essential] => false [longName] => --singleton [longAname] => [shortAname] => [shortName] => -ts [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export the list of variants having only one minor allele. Note that the definition of 'having no minor allele' might be depends on the dataset or filters applied. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export the list of variants having only one minor allele. Note that the definition of 'having no minor allele' might be depends on the dataset or filters applied. ) [doubleton] => Array ( [is_given_default] => false [is_essential] => false [longName] => --doubleton [longAname] => [shortAname] => [shortName] => -tb [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export the list of variants having only two minor allele. Note that the definition of 'having no minor allele' might be depends on the dataset or filters applied. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Export the list of variants having only two minor allele. Note that the definition of 'having no minor allele' might be depends on the dataset or filters applied. ) [genemdr] => Array ( [is_given_default] => false [is_essential] => false [longName] => --genemdr [longAname] => [shortAname] => [shortName] => -Gm [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Perform Gene-based MDR. [optExcl] => * [optRequ] => --set [optWith] => [detaildesc] => Perform Gene-based MDR. ) [variant2cov] => Array ( [is_given_default] => false [is_essential] => false [longName] => --variant2cov [longAname] => [shortAname] => [shortName] => -m2 [defVal] => [optType] => [optCat] => RT_OTHER [desc] => Apply selected variants as covariates. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Apply selected variants as covariates. ) [inbreed] => Array ( [is_given_default] => false [is_essential] => false [longName] => --inbreed [longAname] => [shortAname] => [shortName] => -ib [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Compute sample-wise inbreeding coefficient F. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Compute sample-wise inbreeding coefficient F. ) [group] => Array ( [is_given_default] => false [is_essential] => false [longName] => --group [longAname] => [shortAname] => [shortName] => -g [defVal] => [optType] => file path [optCat] => RT_OTHER [desc] => Define a group for samples or variants [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Define a group for samples or variants ) [filgenic] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filgenic [longAname] => [shortAname] => [shortName] => -fG [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Filtering out all of variants do not reside in genic region, based on the gene range file. [optExcl] => --filintergenic [optRequ] => * [optWith] => [detaildesc] => Filtering out all of variants do not reside in genic region, based on the gene range file. ) [filintergenic] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filintergenic [longAname] => [shortAname] => [shortName] => -fI [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Filtering out all of variants do not reside in intergenic region, based on the gene range file. [optExcl] => --filgenic [optRequ] => * [optWith] => [detaildesc] => Filtering out all of variants do not reside in intergenic region, based on the gene range file. ) [variantsummary] => Array ( [is_given_default] => false [is_essential] => false [longName] => --variantsummary [longAname] => [shortAname] => [shortName] => -ks [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Write out a comprehensive summary for variants, in a chromosome-wise manner. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Write out a comprehensive summary for variants, in a chromosome-wise manner. ) [sampleorder] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sampleorder [longAname] => [shortAname] => [shortName] => -sO [defVal] => [optType] => A path of file contains new sample order [optCat] => RT_OTHER [desc] => Re-ordering samples with specific order, as listed in file. Non-existing samples in the order file will be ignored. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Re-ordering samples with specific order, as listed in file. Non-existing samples in the order file will be ignored. ) [variantorder] => Array ( [is_given_default] => false [is_essential] => false [longName] => --variantorder [longAname] => [shortAname] => [shortName] => -sM [defVal] => [optType] => A path of file contains new variant order [optCat] => RT_OTHER [desc] => Re-ordering variants with specific order, as listed in file. Non-existing variants in the order file will be ignored. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Re-ordering variants with specific order, as listed in file. Non-existing variants in the order file will be ignored. ) [cosi] => Array ( [is_given_default] => false [is_essential] => false [longName] => --cosi [longAname] => [shortAname] => [shortName] => -co [defVal] => [optType] => [optCat] => RT_OTHER [desc] => Convert the final dataset to the format that can be accepted in COSI program. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Convert the final dataset to the format that can be accepted in COSI program. ) [setconsec] => Array ( [is_given_default] => false [is_essential] => false [longName] => --setconsec [longAname] => [shortAname] => [shortName] => -xc [defVal] => 0 [optType] => Positive integer [optCat] => RT_POS [desc] => Automatically generates gene-variant relationship by binding consecutive k variants. [optExcl] => --set [optRequ] => * [optWith] => --setoverlap [detaildesc] => Automatically generates gene-variant relationship by binding consecutive k variants. ) [setoverlap] => Array ( [is_given_default] => false [is_essential] => false [longName] => --setoverlap [longAname] => [shortAname] => [shortName] => -xv [defVal] => 0 [optType] => OT_NUMBER [optCat] => RT_NONNEG [desc] => Set the size of overlap when generating set [optExcl] => --set [optRequ] => --setconsec [optWith] => * ) [setrandom] => Array ( [is_given_default] => false [is_essential] => false [longName] => --setrandom [longAname] => [shortAname] => [shortName] => -xr [defVal] => [optType] => OT_RANGE [optCat] => RT_POS [desc] => Automatically generate set with random variants ) [makeset] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makeset [longAname] => [shortAname] => [shortName] => -mS [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Export retrieved and matched gene-variant relationship as file, non-existing variants in final dataset or the gene does not have any existing variants will be removed. [optExcl] => * [optRequ] => --set/--setconsec [optWith] => [detaildesc] => Export retrieved and matched gene-variant relationship as file, non-existing variants in final dataset or the gene does not have any existing variants will be removed. ) [settype] => Array ( [is_given_default] => false [is_essential] => false [longName] => --settype [longAname] => [shortAname] => [shortName] => -et [defVal] => 0 [optType] => One of 1,2,3,4,5 [optCat] => RT_POS [desc] => Determine the type of exported gene-variant relationship. [optExcl] => * [optRequ] => --makeset,--set/--setconsec [optWith] => [detaildesc] => Determine the type of exported gene-variant relationship. ) [outcact] => Array ( [is_given_default] => false [is_essential] => false [longName] => --outcact [longAname] => [shortAname] => [shortName] => -oc [defVal] => [optType] => Two integers separated by comma(,) w/o whitespace [optCat] => RT_OTHER [desc] => Determine character for case/control when generate dataset file from final dataset. [optExcl] => --out1case [optRequ] => Export-related options [optWith] => [detaildesc] => Determine character for case/control when generate dataset file from final dataset. ) [out1case] => Array ( [is_given_default] => false [is_essential] => false [longName] => --out1case [longAname] => [shortAname] => [shortName] => -o1 [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Determine character for case/control as 1/0 respectively, when generate dataset from final dataset. Equivalent to --outcact 1,0 [optExcl] => --outcact [optRequ] => Export-related options [optWith] => [detaildesc] => Determine character for case/control as 1/0 respectively, when generate dataset from final dataset. Equivalent to --outcact 1,0 ) [mistest] => Array ( [is_given_default] => false [is_essential] => false [longName] => --mistest [longAname] => [shortAname] => [shortName] => -mt [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Perform a test for genotype missingness is random or not. [optExcl] => * [optRequ] => --miss [optWith] => [detaildesc] => Perform a test for genotype missingness is random or not. ) [incmistest] => Array ( [is_given_default] => false [is_essential] => false [longName] => --incmistest [longAname] => [shortAname] => [shortName] => -iM [defVal] => [optType] => range (0~1) [optCat] => RT_01 [desc] => Include variants only having its p-value of random missingness test from case-control data is within range [optExcl] => --filmistest [optRequ] => --mistest [optWith] => [detaildesc] => Include variants only having its p-value of random missingness test from case-control data is within range ) [filmistest] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filmistest [longAname] => [shortAname] => [shortName] => -fM [defVal] => [optType] => range (0~1) [optCat] => RT_01 [desc] => Exclude variants having its p-value of random missingness test from case-control data is within range [optExcl] => --incmistest [optRequ] => --mistest [optWith] => [detaildesc] => Exclude variants having its p-value of random missingness test from case-control data is within range ) [nageno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nageno [longAname] => [shortAname] => [shortName] => -Ng [defVal] => [optType] => Positive integer(number of genotypes) or real number (0,1) (proportion of genotypes) [optCat] => RT_NONNEG [desc] => Generate given proportion of missingness to the dataset(if an argument is a real number between 0~1), or specific number of missing genotype to the dataset(if an argument is an integer more than 1) [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Generate given proportion of missingness to the dataset(if an argument is a real number between 0~1), or specific number of missing genotype to the dataset(if an argument is an integer more than 1) ) [napheno] => Array ( [is_given_default] => false [is_essential] => false [longName] => --napheno [longAname] => [shortAname] => [shortName] => -NH [defVal] => [optType] => OT_REAL [optCat] => RT_NONNEG [desc] => Make given portion or number of phenotype as missing ) [filtreport] => Array ( [is_given_default] => false [is_essential] => false [longName] => --filtreport [longAname] => [shortAname] => [shortName] => -fr [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Write out a report for the filtered-out samples about which reason was they have filtered out. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Write out a report for the filtered-out samples about which reason was they have filtered out. ) [ggemma] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ggemma [longAname] => [shortAname] => [shortName] => -zg [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Perform gene-level GEMMA test. [optExcl] => * [optRequ] => --genetest,--set/--setconsec [optWith] => [detaildesc] => Perform gene-level GEMMA test. ) [fisher] => Array ( [is_given_default] => false [is_essential] => false [longName] => --fisher [longAname] => [shortAname] => [shortName] => -fy [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Perform variant-level Fisher's Exact test using final dataset. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform variant-level Fisher's Exact test using final dataset. ) [trend] => Array ( [is_given_default] => false [is_essential] => false [longName] => --trend [longAname] => [shortAname] => [shortName] => -CA [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Perform variant-level Cochran-Armitage trend test using final dataset. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Perform variant-level Cochran-Armitage trend test using final dataset. ) [genofield] => Array ( [is_given_default] => false [is_essential] => false [longName] => --genofield [longAname] => [shortAname] => [shortName] => -gf [defVal] => [optType] => String with no whitespace [optCat] => RT_OTHER [desc] => Define the name of field containing hard-coded genotype in number. When this option is assigned, a default field for recognizing genotype will be ignored. [optExcl] => * [optRequ] => --vcf [optWith] => [detaildesc] => Define the name of field containing hard-coded genotype in number. When this option is assigned, a default field for recognizing genotype will be ignored. ) [outphenoonly] => Array ( [is_given_default] => false [is_essential] => false [longName] => --outphenoonly [longAname] => [shortAname] => [shortName] => -oo [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => When generate dataset in specific format from final dataset, only export phenotype if the format includes FID, IID, parental relationship and sex. [optExcl] => * [optRequ] => --makeraw/--makedom/--makerec [optWith] => [detaildesc] => When generate dataset in specific format from final dataset, only export phenotype if the format includes FID, IID, parental relationship and sex. ) [outnoheader] => Array ( [is_given_default] => false [is_essential] => false [longName] => --outnoheader [longAname] => [shortAname] => [shortName] => -on [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => When generate dataset in specific format from final dataset, do not export its header if the format includes header. [optExcl] => * [optRequ] => --makeraw/--makedom/--makerec [optWith] => [detaildesc] => When generate dataset in specific format from final dataset, do not export its header if the format includes header. ) [makemerlin] => Array ( [is_given_default] => false [is_essential] => false [longName] => --makemerlin [longAname] => [shortAname] => [shortName] => -om [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Convert the final dataset to the format that can be accepted in MERLIN program. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Convert the final dataset to the format that can be accepted in MERLIN program. ) [emmax] => Array ( [is_given_default] => false [is_essential] => false [longName] => --emmax [longAname] => [shortAname] => [shortName] => -ex [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Perform EMMAX ) [mds] => Array ( [is_given_default] => false [is_essential] => false [longName] => --mds [longAname] => [shortAname] => [shortName] => -MD [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Generate MDS plot points and draw if possible ) [gxg] => Array ( [is_given_default] => false [is_essential] => false [longName] => --gxg [longAname] => [shortAname] => [shortName] => -gg [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Performs GxG interaction test in regression analysis. Note that only two-way interaction will be assessed. [detaildesc] => Performs GxG interaction test in regression analysis. Note that only two-way interaction will be assessed. ) [invnorm] => Array ( [is_given_default] => false [is_essential] => false [longName] => --invnorm [longAname] => [shortAname] => [shortName] => -vn [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Apply inverse-normalization transformation for given phenotype. Note that this option does not affects to the dichotomous phenotype and factor-type phenotype. [optExcl] => --phenostdize [optRequ] => * [optWith] => [detaildesc] => Apply inverse-normalization transformation for given phenotype. Note that this option does not affects to the dichotomous phenotype and factor-type phenotype. ) [fst] => Array ( [is_given_default] => false [is_essential] => false [longName] => --fst [longAname] => [shortAname] => [shortName] => -Ft [defVal] => [optType] => [optCat] => RT_OTHER [desc] => Compute Fst for each marker. Note that gene-wise Fst will be computed with --set. [optExcl] => * [optRequ] => * [optWith] => [detaildesc] => Compute Fst for each marker. Note that gene-wise Fst will be computed with --set. ) [forceconv] => Array ( [is_given_default] => false [is_essential] => false [longName] => --forceconv [longAname] => [shortAname] => [shortName] => -fV [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Forcely converge LMM ) [out1234] => Array ( [is_given_default] => false [is_essential] => false [longName] => --out1234 [longAname] => [shortAname] => [shortName] => -t1 [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => In the export of non-binarized format, change A/C/G/T into 1/2/3/4, respectively. [optExcl] => --outacgt [optRequ] => * [optWith] => [detaildesc] => In the export of non-binarized format, change A/C/G/T into 1/2/3/4, respectively. ) [outacgt] => Array ( [is_given_default] => false [is_essential] => false [longName] => --outacgt [longAname] => [shortAname] => [shortName] => -oa [defVal] => [optType] => Four characters corresponding to A, C, G, T, respectively [optCat] => RT_OTHER [desc] => In the export of non-binarized format, change A/C/G/T into given four characters, respectively. [optExcl] => --out1234 [optRequ] => * [optWith] => [detaildesc] => In the export of non-binarized format, change A/C/G/T into given four characters, respectively. ) [genesplit] => Array ( [is_given_default] => false [is_essential] => false [longName] => --genesplit [longAname] => [shortAname] => [shortName] => -GS [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Split the dataset by gene-marker mapping. [optExcl] => * [optRequ] => --set/--setconsec [optWith] => [detaildesc] => Split the dataset by gene-marker mapping. ) [dfam] => Array ( [is_given_default] => false [is_essential] => false [longName] => --dfam [longAname] => [shortAname] => [shortName] => -da [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Perform DFAM analysis, initially suggested in PLINK. [detaildesc] => Perform DFAM analysis, initially suggested in PLINK. ) [updallele] => Array ( [is_given_default] => false [is_essential] => false [longName] => --updallele [longAname] => [shortAname] => [shortName] => -ua [defVal] => [optType] => File path [optCat] => RT_OTHER [desc] => Update allele information ) [window] => Array ( [is_given_default] => false [is_essential] => false [longName] => --window [longAname] => [shortAname] => [shortName] => -W [defVal] => 0 [optType] => Positive integer > 1 [optCat] => RT_POS [desc] => Set the window for various options [optExcl] => * [optRequ] => * [optWith] => --filfreq,--filmac,--filhwe,--filgvar,--filgdist,--filqual ) [ci] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ci [longAname] => [shortAname] => [shortName] => -ci [defVal] => 0.05 [optType] => [optCat] => RT_01 [desc] => Print out confidence interval if available ) [lasso] => Array ( [is_given_default] => false [is_essential] => false [longName] => --lasso [longAname] => [shortAname] => [shortName] => -la [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Performs LASSO regression with gene-marker mapping file. [detaildesc] => Performs LASSO regression with gene-marker mapping file. ) [lassolambda] => Array ( [is_given_default] => false [is_essential] => false [longName] => --lassolambda [longAname] => [shortAname] => [shortName] => -ll [defVal] => 0.1 [optType] => Real value [optCat] => RT_POS [desc] => Cut lambda value for LASSO ) [lassoall] => Array ( [is_given_default] => false [is_essential] => false [longName] => --lassoall [longAname] => [shortAname] => [shortName] => -lL [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Performs LASSO regression and reports all variables in the set. [detaildesc] => Performs LASSO regression and reports all variables in the set. ) [pls] => Array ( [is_given_default] => false [is_essential] => false [longName] => --pls [longAname] => [shortAname] => [shortName] => -ps [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Perform regression with partial least square (PLS) ) [sampleweight] => Array ( [is_given_default] => false [is_essential] => false [longName] => --sampleweight [longAname] => [shortAname] => [shortName] => -sw [defVal] => [optType] => File path [optCat] => RT_OTHER [desc] => Provide sample-wise weight for LMM ) [rvtdt] => Array ( [is_given_default] => false [is_essential] => false [longName] => --rvtdt [longAname] => [shortAname] => [shortName] => -rd [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Performs rv-TDT analysis, a TDT-based gene-level test for family data. [detaildesc] => Performs rv-TDT analysis, a TDT-based gene-level test for family data. ) [fbskat] => Array ( [is_given_default] => false [is_essential] => false [longName] => --fbskat [longAname] => [shortAname] => [shortName] => -fK [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Performs FB-SKAT analysis, a SKAT-based gene-level test for family data. [detaildesc] => Performs FB-SKAT analysis, a SKAT-based gene-level test for family data. ) [nskip] => Array ( [is_given_default] => false [is_essential] => false [longName] => --nskip [longAname] => [shortAname] => [shortName] => -nk [defVal] => [optType] => Positive integer [optCat] => RT_POS [desc] => Skips first k lines from main dataset file, such as .ped, .lgen, .tped files. [detaildesc] => Skips first k lines from main dataset file, such as .ped, .lgen, .tped files. ) [singleparent] => Array ( [is_given_default] => false [is_essential] => false [longName] => --singleparent [longAname] => [shortAname] => [shortName] => -sP [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Allow single-side parent in the retrieval of pedigree structure ) [bcf] => Array ( [is_given_default] => false [is_essential] => false [longName] => --bcf [longAname] => [shortAname] => [shortName] => -B [defVal] => [optType] => File path [optCat] => RT_OTHER [desc] => Retrieve BCF file as an input [optExcl] => --vcf,--tped,--ped,--dosage,--bed,--simtrio,--lgen,--simfam,--variantvar [optRequ] => * [optWith] => --filqual,--vcfqc ) [loocv] => Array ( [is_given_default] => false [is_essential] => false [longName] => --loocv [longAname] => [shortAname] => [shortName] => -lv [defVal] => [optType] => [optCat] => RT_ONOFF [desc] => Performs Leave-one-out cross-validation (LOOCV) in the analysis. [optExcl] => --cv [optRequ] => --mdr [optWith] => * [detaildesc] => Performs Leave-one-out cross-validation (LOOCV) in the analysis. ) [mdrthr] => Array ( [is_given_default] => false [is_essential] => false [longName] => --mdrthr [longAname] => [shortAname] => [shortName] => -dt [defVal] => [optType] => Real value ranged (0,1] [optCat] => RT_01 [desc] => MDR reporting threshold [optExcl] => * [optRequ] => --mdr [optWith] => * ) [ldcontrast] => Array ( [is_given_default] => false [is_essential] => false [longName] => --ldcontrast [longAname] => [shortAname] => [shortName] => -lx [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Perform LD contrast method ) [flip] => Array ( [is_given_default] => false [is_essential] => false [longName] => --flip [longAname] => [shortAname] => [shortName] => -fL [defVal] => TGCA [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Flip the genotype or change with custom flip order ) [varsubset] => Array ( [is_given_default] => false [is_essential] => false [longName] => --varsubset [longAname] => [shortAname] => [shortName] => -fT [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Assign a list of variants to be flipped ) [hethom] => Array ( [is_given_default] => false [is_essential] => false [longName] => --hethom [longAname] => [shortAname] => [shortName] => -hh [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Compute sample-site het/hom ratio [optExcl] => * [optRequ] => * [optWith] => * ) [markercheck] => Array ( [is_given_default] => false [is_essential] => false [longName] => --markercheck [longAname] => [shortAname] => [shortName] => -mk [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Validate marker information based on dbSNP ) [meta] => Array ( [is_given_default] => false [is_essential] => false [longName] => --meta [longAname] => [shortAname] => [shortName] => -p [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Perform meta-analysis ) [fid] => Array ( [is_given_default] => false [is_essential] => false [longName] => --fid [longAname] => [shortAname] => [shortName] => -xf [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Force FID to fixed one ) [outformat] => Array ( [is_given_default] => false [is_essential] => false [longName] => --outformat [longAname] => [shortAname] => [shortName] => -of [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Output type of table type outputs ) [maf] => Array ( [is_given_default] => false [is_essential] => false [longName] => --maf [longAname] => [shortAname] => [shortName] => -ma [defVal] => [optType] => range (0~0.5] [optCat] => RT_OTHER [desc] => Pre-defined MAF ) [het] => Array ( [is_given_default] => false [is_essential] => false [longName] => --het [longAname] => [shortAname] => [shortName] => -ht [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Compute heterozygosity ) [variantblup] => Array ( [is_given_default] => false [is_essential] => false [longName] => --variantblup [longAname] => [shortAname] => [shortName] => -vp [defVal] => [optType] => OT_REAL [optCat] => RT_POS [desc] => Compute variant-level BLUP ) [famsplit] => Array ( [is_given_default] => false [is_essential] => false [longName] => --famsplit [longAname] => [shortAname] => [shortName] => -FS [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Export final dataset by FID ) [setspan] => Array ( [is_given_default] => false [is_essential] => false [longName] => --setspan [longAname] => [shortAname] => [shortName] => -sn [defVal] => 0 [optType] => OT_NUMBER [optCat] => RT_NONNEG [desc] => Gene plus-minus span for mapping variant when gene definition is ranged form ) [tridge] => Array ( [is_given_default] => false [is_essential] => false [longName] => --tridge [longAname] => [shortAname] => [shortName] => -tr [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Perform truncated ridge analysis ) [hamming] => Array ( [is_given_default] => false [is_essential] => false [longName] => --hamming [longAname] => [shortAname] => [shortName] => -hn [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Calculate relatedness matrix using Hamming distance ) [baldingnichols] => Array ( [is_given_default] => false [is_essential] => false [longName] => --baldingnichols [longAname] => [shortAname] => [shortName] => -bn [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Calculate relatedness matrix using Balding-Nichols model ) [fuzzymdr] => Array ( [is_given_default] => false [is_essential] => false [longName] => --fuzzymdr [longAname] => [shortAname] => [shortName] => -zm [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Perform fuzzy MDR analysis ) [gxgall] => Array ( [is_given_default] => false [is_essential] => false [longName] => --gxgall [longAname] => [shortAname] => [shortName] => -gX [defVal] => [optType] => OT_ONOFF [optCat] => RT_ONOFF [desc] => Perform GxG analysis with all variables into a single model ) [gxglist] => Array ( [is_given_default] => false [is_essential] => false [longName] => --gxglist [longAname] => [shortAname] => [shortName] => -xl [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => List of gene pairs to test gene-gene interaction ) [gxglambda] => Array ( [is_given_default] => false [is_essential] => false [longName] => --gxglambda [longAname] => [shortAname] => [shortName] => -xb [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => List of lambdas of gene/pathway to try for gene-gene interaction ) [prunevif] => Array ( [is_given_default] => false [is_essential] => false [longName] => --prunevif [longAname] => [shortAname] => [shortName] => -rv [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Prune variants by Variance Inflation Factor ) [prunepw] => Array ( [is_given_default] => false [is_essential] => false [longName] => --prunepw [longAname] => [shortAname] => [shortName] => -rw [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Prune variants by pair-wise manner ) [selgene] => Array ( [is_given_default] => false [is_essential] => false [longName] => --selgene [longAname] => [shortAname] => [shortName] => -gn [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Select genes with given expression ) [remgene] => Array ( [is_given_default] => false [is_essential] => false [longName] => --remgene [longAname] => [shortAname] => [shortName] => -en [defVal] => [optType] => OT_STRING [optCat] => RT_OTHER [desc] => Remove genes with given expression ) [ption] => Array ( [optExcl] => #excl [optRequ] => #req [optWith] => #with ) [simfam] => Array ( [optExcl] => --tped,--ped,--dosage,--bed,--vcf,--lgen,--simtrio [optRequ] => * [optWith] => [desc] => Generate input by simulation, under given pedigree structure [detaildesc] => Generate input by simulation, under given pedigree structure [optType] => ) [szfam] => Array ( [optExcl] => --tped,--ped,--dosage,--bed,--vcf,--lgen [optRequ] => --simtrio,--simfam [optWith] => [desc] => Set the number of families simulated [detaildesc] => Set the number of families simulated [optType] => positive integer ) [usepp] => Array ( [optExcl] => * [optRequ] => * [optWith] => * [desc] => Perform the analyses with utilization of missing-founders, which are not included in the dataset but in the pedigree structure [detaildesc] => Perform the analyses with utilization of missing-founders, which are not included in the dataset but in the pedigree structure [optType] => ) [filfreq] => Array ( [optExcl] => --incfreq [optRequ] => --freq,--freq≠corr [optWith] => --window [desc] => Exclude all variants satisfying the condition that the MAF is in specified range [detaildesc] => Exclude all variants satisfying the condition that the MAF is in specified range [optType] => range (0~1) ) [filpheno] => Array ( [optExcl] => --incpheno [optRequ] => * [optWith] => --sampvar,--pname [desc] => Filtering samples based on the condition related to phenotype [detaildesc] => Filtering samples based on the condition related to phenotype [optType] => string ) [incfreq] => Array ( [optExcl] => --filfreq [optRequ] => * [optWith] => * [desc] => Include the variants that satisfying its MAF in given range only to the analyses [detaildesc] => Include the variants that satisfying its MAF in given range only to the analyses [optType] => range (0~1) ) [gsmissthr] => Array ( [optExcl] => * [optRequ] => * [optWith] => * [desc] => Exclude variant from the gene-level analysis if its missingness rate above than the threshold [detaildesc] => Exclude variant from the gene-level analysis if its missingness rate above than the threshold [optType] => real number (0~1) ) [cormaf] => Array ( [optExcl] => * [optRequ] => * [optWith] => --ibs/--corpearson/--ktau/--empktau/--empiall/--medcor [desc] => Determine the range of MAF to be incorporated to empirical correlation computation [detaildesc] => Determine the range of MAF to be incorporated to empirical correlation computation [optType] => range (0~1) ) [qtestrange] => Array ( [optExcl] => * [optRequ] => --qtest [optWith] => [desc] => Define the range of variant's MAF to performing Q-test [detaildesc] => Define the range of variant's MAF to performing Q-test [optType] => range (0~1) ) [filcov] => Array ( [optExcl] => --inccov [optRequ] => --pheno,--cname [optWith] => * [desc] => Like --filpheno, filtering out samples that satisfying specific condition on their covariates [detaildesc] => Like --filpheno, filtering out samples that satisfying specific condition on their covariates [optType] => string expression ) [incpheno] => Array ( [optExcl] => --filpheno [optRequ] => * [optWith] => --pheno,--pname [desc] => Include only the samples satisfying the condition related to phenotype [detaildesc] => Include only the samples satisfying the condition related to phenotype [optType] => string expression ) [inccov] => Array ( [optExcl] => --filcov [optRequ] => --pheno,--cname [optWith] => * [desc] => Like --filcov, include only the samples that satisfying specific condition on their covariates [detaildesc] => Like --filcov, include only the samples that satisfying specific condition on their covariates [optType] => string expression ) [lassolabmda] => Array ( [desc] => Set the threshold for reporting of variables in LASSO regression analysis. [detaildesc] => Set the threshold for reporting of variables in LASSO regression analysis. ) )

Edit this page
Last modified : 2013-09-23 21:59:20