sampleQC {UKB.COVID19}

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csv file with withdrawn IDs from UK Biobank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)