WISARD official site

Select O/S : [?]

Case tutorial

Detail of [AI.blup]

An estimation of BLUP using EM-AI algorithm for REML model

Output format is TSV

Column	Format	Modifier
FID	--makeblup,--pname	Predicted value of the phenotype
IID	--makeblup,--pname	Predicted value of the phenotype
BLUP_(phenotype name)	--makeblup,--pname	Predicted value of the phenotype
PRED_(phenotype name)	--makeblup,--pname	Predicted value of the phenotype

Output Index

Here is the list of all outputs produced from WISARD.

Suffix	Format	Produced by	Affected by	Description
log	arbitrary	NONE	--verbose	A complete log file produced from an execution of WISARD
gene.res	TSV	--genetest	--skat --skato --pedcmc	A result of gene-level test (Burden, SKAT, SKAT-o, PEDCMC)
simple.qls.res	TSV	--qls	NONE	A result of QLS analysis
extended.qls.res	TSV	--mfqls	--mqlsconsec	A result of Extended QLS analysis
all.hwe	TSV	--hwe all	NONE	A computed HWE using all samples
founders.hwe	TSV	--hwe founder	NONE	A computed HWE using only founder samples
sampvar.res	TSV	--sxa	NONE	A result of computation of conditional variance for each sample
top.sampvar.res	TSV	--sxa	--nsamp An ascending-sorted result of conditional variances
AI.blup	TSV	--makeblup	--nostop --emcount --aithr	An estimation of BLUP using EM-AI algorithm for REML model
NR.blup	TSV	--makeblup --ml	--nostop --emcount	An estimation of BLUP using Newton-Raphson algorithm for ML model
SD.blup	TSV	--makeblup --specdcmp	NONE	An estimation of BLUP using spectral decomposition
trend.res	TSV	--trend	NONE	A result of Cochran-Armitage trend test and allelic based test for the testing of association in case/control dataset
fisher.res	TSV	--fisher	NONE	A result of Fisher's exact test for the testing of association in case/control dataset
summary.variant.res	TSV	--variantsummary	NONE	A chromosome-wise summary for the various information from variants
tstv.variant.lst	TSV	--tstv	NONE	A result of Ts/Tv ratio by window
tstv.chr.lst	TSV	--tstv	NONE	A result of Ts/Tv ratio by chromosome
mistest.res	TSV	--mistest binary phenotype	NONE	A result of test of random missingness between case/control
inbreed.coef.res	TSV	--inbreed	NONE	A result of computation of inbreeding coefficient F
lod.res	TSV	--lod	NONE	A result of Log of Odds analysis
mendel.sample.res	TSV	--mendel	NONE	A result of analysis of sample-wise Mendelian transmission error
mendel.variant.res	TSV	--mendel	NONE	A result of analysis of variant-wise Mendelian transmission error
mendel.family.res	TSV	--mendel	NONE	A result of analysis of family-wise Mendelian transmission error
sample.miss.lst	TSV	--miss	NONE	A report of genotype missingness per sample
variant.miss.lst	TSV	--miss	NONE	A report of genotype missingness per variant
family.miss.lst	TSV	--miss	NONE	A report of genotype missingness per family
tdt.res	TSV	--tdt	NONE	A result of Transmission Disequilibrium Test
sdt.res	TSV	--sdt	NONE	A result of Sibship Disequilibrium Test
fst.res	TSV	--fst	--set	A result of F_ST estimation
variant.popuniq.res	TSV	--popuniq	NONE	A list of population-specific variants
variant.famuniq.res	TSV	--famuniq	NONE	A list of family-specific variants
variant.singleton.res	TSV	--singleton	NONE	A list of singleton variants (it means, there is only 'one' sample who having variant allele in a variant across final dataset)
variant.monotone.res	TSV	--monotone	NONE	A list of monotone variants (it means, there is no sample who having variant allele in a variant across final dataset)
variant.doubleton.res	TSV	--doubleton	NONE	A list of doubleton variants (it means, there is only 'two' sample who having variant allele in a variant across final dataset)
gene.fail.lst	LIST	--genetest	--skato	A list of gene names that failed to perform SKAT-o test
filter.sample.lst	TSV	--incgeno --filgeno	NONE	A list of sample filtering status by filtering criteria
allmiss.sample.lst	TSV	NONE	NONE	A list of samples having NO available genotype
linear.regr.res	TSV	--regression	--interaction	A result of regression analysis with continuous phenotype
logistic.regr.res	TSV	--regression	--interaction	A result of regression analysis with dichotomous phenotype
family.qls.res	TSV	--fqls	--mqls --avail --fqlsnopddt --retestthr	A result of Family QLS analysis
estimated.maf	TSV	--freq corr	NONE	An estimated MAF from sample relatedness
all.maf	TSV	--freq all	NONE	A computed MAF using all samples
founders.maf	TSV	--freq founder	NONE	A computed MAF using only founder samples
power.single.res	TSV	--powercalc	NONE	A result of power calculation from single phenotype
power.multi.res	TSV	--powercalc	NONE	A result of power calculation from multiple phenotypes
miss.pheno.lst	TSV	NONE	--sampvar --pname	A list of samples having phenotype missingness
miss.sex.lst	TSV	NONE	NONE	A list of samples having sex missingness
summary.gene.lst	TSV	--genetest --genesummary	NONE	A summary of analyzed gene-variant information
summary.gmap.lst	TSV	--genetest --gmapsummary Single binary phenotype	NONE	A summary of variant distribution across case-control samples for each gene mapping
entire.dist.dsg	TSV	--dsgdist	NONE	A distribution of dosage for entire dataset
sample.dist.dsg	TSV	--dsgdist	NONE	A sample-wise distribution of dosage
ibs.cor	matrix/TSV	--ibs	--cormat	A matrix/list of pairs that contains computed IBS
empi.cor	matrix/TSV	--makecor	--cormat	A matrix/list of pairs that contains computed empirical kinship coefficients
empi.med.cor	matrix/TSV	--makecor --medcor	--cormat	A matrix/list of pairs that contains computed median of empirical kinship coefficients
theo.cor	matrix/TSV	--pddt	--cormat	A matrix/list of pairs that contains computed theoretical kinship coefficients based on the pedigree structure
hybrid.cor	matrix/TSV	--hybrid	--cormat	A matrix/list of pairs that contains mixed kinship coefficients
pearson.cor	matrix/TSV	--corpearson	--cormat	A matrix/list of pairs that contains Pearson's correlation coefficients
ktau.cor	matrix/TSV	--ktau	--cormat	A matrix/list of pairs that contains Kendall's tau correlation coefficients from raw genotype data
empi.ktau.cor	matrix/TSV	--empiktau	--cormat	A matrix/list of pairs that contains Kendall's tau correlation coefficients from normalized genotype data
ped	PLINK PED	--makeped	NONE	PED-formatted output of filtered dataset
map	PLINK MAP	--makeped --makelgen	NONE	MAP-formatted output of filtered dataset, accompanied by ped(--makeped) or lgen(--makelgen)
tped	PLINK transposed PED	--maketped	NONE	Transposed PED-formatted output of filtered dataset
tfam	PLINK FAM	--maketped	NONE	FAM-formatted output of filtered dataset, accompanied by tped
lgen	Long-format dataset	--makelgen	NONE	Long-formatted output of filtered dataset
vcf	VCF	--makevcf	NONE	VCF output of filtered dataset
bed	PLINK binary PED	--makebed	NONE	BED-formatted output of filtered dataset
bim	PLINK FAM	--makebed	NONE	BIM-formatted output of filtered dataset, accompanied by bed
fam	PLINK FAM	--makevcf --makebed --makelgen	NONE	FAM-formatted output of filtered dataset, accompanied by bed(--makebed) or lgen(--makelgen)
raw	PLINK RAW	--makeraw --makedom --makerec	NONE	RAW-formatted output of filtered dataset, additive-coded genotype
structure.fam	ARBITRARY	--famsummary	NONE	A report of retrieved pedigree structure
structure.nucl.fam	ARBITRARY	--ncsummary	NONE	A report of retrieved pedigree structure by nuclear family
qtest.res	TSV	--qtest	NONE	A result of Q-test
gemma.res	TSV	--femma	NONE	A result of GEMMA
mdr.res	TSV	--mdr	NONE	A result of MDR
pca.res	TSV	--pca	--npc	A list of computed PC scores
density.variant.lst	TSV	--density	NONE	A result of physical variant density by window
scoretest.res	TSV	--scoretest	--lrt --pddt	A result of Score test
covar.mat	TSV	--makecov	--sampvar --cname --baseline	A matrix of covariates that actually used in the analyses, constructed from given covariates and final dataset
pheno.mat	TSV	--makepheno	--sampvar --pname	A matrix of phenotype(s) that actually used in the analyses, constructed from given phenotypes and final dataset
poly.est.res	table	--heritability	--ml --specdcmp --aithr	A result of heritability estimation
altcor.miss.lst	LIST	--cor	NONE	A list of sample IDs consists of the samples not included in the final dataset, but exists in the alternative correlation file
samplist.miss.lst	LIST	--remsamp/--selsamp	NONE	A list of sample IDs consists of the samples not included in the final dataset, but exists in the sample list file
stat.sample.lst	TSV	NONE	NONE	A report of samples about whether sample is included in the final dataset or not, and the reason of the sample was not included if it was not included
gen	GEN	--makegen	NONE	GEN-formatted output of filtered dataset
sample	SAMPLE	--makegen/--makebgen	NONE	Sample information of GEN-formatted output
bgen	Binary GEN	--makebgen	NONE	Binarized GEN-formatted output of filtered dataset
variant.lst	TSV	--listvariant	NONE	A list of variant IDs that actually included in the final dataset
sample.lst	TSV	--listsample	NONE	A list of sample IDs that actually included in the final dataset
founder.lst	TSV	--listfounder	NONE	A list of founder sample IDs that actually included in the final dataset
allelic.excl.lst	LIST	--vcf	NONE	A list of variant IDs of the variants excluded before an analysis due to it contains more than two alleles (triallelic or polyallelic)
set.gene.lst	LIST	--makeset	--settype	Gene-marker definition formatted set after mapping between original gene-marker definition and final dataset

Edit this page

Last modified : 2022-09-08 17:16:37