filter_genocall: Function to filter out variants in the genotype hard call...

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 filtler out variants by (1) duplicated position, (2) homozygous genotype for all samples, (3) missing rate greater than given missing-cut and (4) given maf.

Usage

filter_genocall(geno, snps, missing_cut = 0.5, maf_cut = 0.05, common = T)

Arguments

geno	additive coding genotype files, it is the .raw file in plink with 6th columns are phenotype data (output of geno_add_2pheno if no phenotype)
snps	a matrix of the variant informations including at least chr, position, alternative and reference alleles
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.