W-test: dataset adaptive association test for main and interaction effects in GWAS data

JC School of Public Health and Primary Care (JC SPHPC)  |  Faculty of Medicine |  The Chinese University of Hong Kong (CUHK)  |  Hong Kong SAR







      - R

      - C++

      - Linux






  News: wtest is updated in CRAN!

wtest - R package download Version 3.3 (Developer: Rui Sun /Updated 06 Sep 2019)

Also available in CRAN:   install.packages("wtest")

Main function:  wtest(data, y, w.order = c(1, 2), hf1 = "default.hf1", hf2 = "default.hf2", which.pair = NULL, output.pval = NULL, sort = TRUE, input.pval = 0.1, input.poolsize = 50))

Other functions:  maf, odds.ratio, hf.calculation, w.diagnosis (for model diagnosis), w.qqplot

Step by step guide for the R package


wtest  – C++ software (download wtest.exe) (Developer: Junfeng Guo / updated 20 May 2016)

This software is coded using boolean operation (boost method). It is about 30 times faster than the R package.  Sample input genotype file:  genotype.txt (in rows: subjects, in columns: coded SNPs; N x P matrix);  phenotype file: phenotype.txt , (N x 2 matrix, the 1st column is sample ID, and the 2nd column is phenotype).

Step by step guide for C program