variantQC: Variant QC for Genetic Analyses

In UKB.COVID19: UK Biobank COVID-19 Data Processing and Risk Factor Association Tests

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)

UKB.COVID19 documentation built on March 18, 2022, 8:03 p.m.