Functionality Supported by WISARD

Functionalities supported by WISARD can be categorized to (1) study design, (2) data management, (3) quality control and (4) association analysis.

Study design [top]

Basic statistics summarize various information and they are often utilized for quality control. WISARD can calculate

• heritability estimation
• power calculation
• sample selection

Data management [top]

Basic statistics summarize various information and they are often utilized for quality control. WISARD can calculate

• data file conversion, splitting and merging
• data file handling
• imputation of missing data

Quality control [top]

The following statistics can be calculated for quality control with WISARD:

• Minor allele frequency and its distribution
• Minor allele count and its distribution
• Hardy-Weinberg proportion test
• Mendelian-error check
• Variant distribution by chromosomal position
• summary statistics for family, etc

Association analysis [top]

WISARD provides various statistics for detecting genetic association.

• Association analysis
• Chi-square test
• Linear regression
• Logistic regression
• Association analysis under population stratification
• EIGENSTRAT
• Linear mixed model
• Quasi-likelihood score test
• Family-based association analysis
• Wald test for linear mixed model
• Linear mixed model
• Quasi-likelihood score test
• Transmission disequilibrium test
• Epistasis analysis
• Linkage disequilibrium contrast test
• BOOST
• Multifactor dimensionality reduction
• Gene-level association analysis
• CMC test
• KBAC test
• Variable Threshold test
• Weighted sum test
• SKAT method
• SKAT-o method
• Gene-level association analysis under population stratification
• CMC test
• VT test
• Weighted sum test
• SKAT method
• SKAT-o method
• FARVAT test
• Family-based gene-level association analysis
• PedCMC test
• FamVT test
• Weighted sum test
• SKAT method
• SKAT-o method
• FARVAT test
• RV-TDT test
• FB-SKAT method

Analysis Modifiers

WISARD provides several options, which modify conditions for testing and output formats.

Computation time [top]

--time option makes WISARD to report its computational time for each testing unit (variant, gene...). Computational time is reported as msec if a test takes less than one second, and otherwise it is as sec.

Removing NA results from output [top]

--remna option makes WISARD exclude NA results from the output file. Sometimes multiple p-values for a single variant or gene can be calculated. For instance, the association analysis with linear regression can include some covariate effects, and for each variant we have p-values for a given variant and covariates. In this case, if the p-value for a variant is NA, then all results for a given variant are excluded from output files.

Multiple-testing-problem-adjusted p-values [top]

--adjust option provide multiple-testing-problem-adjusted p-values in output files. Note that if there are multiple main p-values, its suffix could be complex, and please check the manual for each analysis for detailed information.

Annotated p-values for each variant [top]

--annogene option produces annotated result for each variant. This option has only one argument which shows a file path with annotation information. This annotation file format can be found at this page.

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