makeGWASFiles: Generate files for GWAS Software. SAIGE and Plink currently...

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

Generate files for GWAS Software. SAIGE and Plink currently supported.

Description

Generate files for GWAS Software. SAIGE and Plink currently supported.

Usage

makeGWASFiles(
  ukb.data,
  pheno,
  covariates,
  phe.name,
  cov.name = NULL,
  includeSampsFile = NULL,
  software = "SAIGE",
  outDir = "",
  prefix
)

Arguments

ukb.data	tab delimited UK Biobank phenotype file, containing sample qc fields (with default UKBiobank codes as column names)
pheno	phenotype dataframe - output from makePhenotype function
covariates	covariate dataframe - output from risk.factor function. Optional.
phe.name	phenotypes to be included in outputted data. multiple phenotypes can be specified as a vector. if null, all phenotypes will be outputted.
cov.name	covariates to be included in outputted data. Optional. multiple covariates can be specified as a vector. if null, all covariates in file will be outputted
includeSampsFile	list of samples to be included GWAS. File with the first column containing sample IDs to be kept. Can contain other columns. output from sampleQC function may be used. Optional - if null, all samples will be outputted.
software	specify "SAIGE" or "plink" - defaults to "SAIGE"
outDir	specify directory to output file
prefix	prefix for file - optional

Value

outputs file, suitable for reading by chosen GWAS software

Examples

## Not run: 
makeGWASFiles(ukb.data=covid_example("sim_ukb.tab.gz"), 
pheno=phe, 
covariates=covar, 
phe.name="hospitalisation", 
cov.name=NULL, 
includeSampsFile=NULL, 
software="SAIGE", 
outDir=covid_example("results"), 
prefix="hospitalisation")

## End(Not run)

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