sampleQC: Sample QC for genetic analyses

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

Sample QC for genetic analyses

Description

Sample QC for genetic analyses

Usage

sampleQC(ukb.data, withdrawnFile, ancestry = "all", software = "SAIGE", outDir)

Arguments

ukb.data	tab delimited UK Biobank phenotype file, containing sample qc fields (with default UKBiobank codes as column names)
withdrawnFile	csv file with withdrawn IDs from UK Biobank
ancestry	specify "WhiteBritish" or "all" - defaults to "all"
software	specify "SAIGE" or "plink" - defaults to "SAIGE"
outDir	specify directory for sample QC file and inclusion/exclusion lists

Value

outputs sample QC file, and sample inclusion / exclusion lists for specified software

Examples

## Not run: 
sampleQC(ukb.data=covid_example("sim_ukb.tab.gz"), 
withdrawnFile=covid_example("sim_withdrawn.csv.gz"), 
ancestry="all", 
software="SAIGE", 
outDir=covid_example("results"))

## End(Not run)

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