filter_snps_samples: Filter loci and samples (requires bcftools and tabix to be...

In FellouMada/rSNPdata: R package for Analysis of P. falciparum whole genome SNPs data

Filter loci and samples (requires bcftools and tabix to be installed)

Description

This function generate the input data needed for whole genome SNP data genotyped from malaria parasite

Usage

snpdata = filter_snps_samples(snpdata, min.qual=10, max.missing.sites=0.2, max.missing.samples=0.2, maf.cutoff=0.01)

Arguments

snpdata	a SNPdata object
min.qual	the minimum call quality score below which a loci will be discarded. default=10
max.missing.sites	the maximum fraction of missing sites above which a sample should be discarded. default=0.2
max.missing.samples	the maximum fraction of missing samples above which a loci should be discarded. default=0.2
maf.cutoff	the MAF cut-off. loci with a MAF < maf.cutoff will be discarded

Value

a SNPdata object

FellouMada/rSNPdata documentation built on June 12, 2022, 7:29 p.m.