geno_process: Function to deal with genotype hard call files in additive...

In Struglab/RVS: Robust Variance Score (RVS) test for association of variants from next generation sequence data with binary traits using external controls

Description

It will read the additive coding genotype file, filter out variants and then return the phenotype and genotype file necessary for association test. It calls functions geno_add_2pheno and filter_genocall

Usage

geno_process(genofile, caseIDfile, missing_cut, maf_cut, common)

Arguments

genofile	additive coding genotype files, it is the .raw file in plink
caseIDfile	the file including the list of case IDs
missing_cut	a decimal, the missing rate cut off
maf_cut	a decimal, the minor allele cut off
common	a boolean variable, common = T, return the variants with maf>=maf_cut, ow, return variants with maf<maf_cut.

Value

a list including- geno: a matrix with the genotype data only (size of nsample*nsnp), snps: matrix with variant information, Y: a vector of phenotype corresponding to the order of the sample in geno, rm_call0: a vector including the position of variants with hom reference calls and rm_miss: a vector including the position of variants with missing_rate>missing_cut in snps after removing rm_call0.

Struglab/RVS documentation built on May 9, 2019, 3:11 p.m.