variantQC {UKB.COVID19}

Variant QC for Genetic Analyses

Description

Variant QC for Genetic Analyses

Usage

variantQC(snpQcFile, mfiDir, mafFilt = 0.001, infoFilt = 0.5, outDir)

Arguments

snpQcFile

file containing SNP QC info (ukb_snp_qc.txt)

mfiDir

directory where the per chromosome UKBiobank MAF/INFO files (ukb_mfi_chr*_v3.txt) are located

mafFilt

minor allele frequency filter - default 0.001

infoFilt

imputation quality (INFO) score filter - default 0.5

outDir

output directory

Value

outputs SNP inclusion lists (SNPID and rsID formats) for given MAF/INFO filters. Also outputs list of SNPs to be used for genetic Relatedness Matrix (GRM) calculations.

Examples

## Not run: 
variantQC(snpQcFile=covid_example("sim_ukb_snp_qc.txt.gz"), 
mfiDir=covid_example("alleleFreqs"), 
mafFilt=0.001, 
infoFilt=0.5, 
outDir=covid_example("results"))

## End(Not run)