makeGWASFiles {UKB.COVID19}

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)