Make_All_Minor_Alleles: Make genotype matrix have MAF<0.5

In lin-lab/CEPSKAT: Finding rare variant associations for extreme phenotype samples.

Usage

Make_All_Minor_Alleles(h, genotypes = FALSE, MAF)

Arguments

h
genotypes
MAF

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (h, genotypes = FALSE, MAF) 
{
    if (genotypes) {
        IDB = which(MAF > 0.5)
        h[, IDB] = 2 - h[, IDB]
        return(as.matrix(h))
    }
    else {
        IDB = which(MAF > 0.5)
        h[, IDB] = 1 - h[, IDB]
        return(as.matrix(h))
    }
  }

lin-lab/CEPSKAT documentation built on May 29, 2019, 3:41 a.m.