mixedVCFtoSnpMatrix {gQTLstats} | R Documentation |
amalgamate called genotypes and imputed allelic dosages in VCF to SnpMatrix representation
mixedVCFtoSnpMatrix(vcf, preferGT = TRUE)
vcf |
object inheriting from |
preferGT |
logical. VCF allows loci for samples to be reported in various
formats, and a given locus can have a call tagged GT and a
genotype probability or likelihood representation tagged GP or GL.
|
emulates output from genotypeToSnpMatrix
list with elements genotypes
and map
VJ Carey
fn = system.file("vcf/polytypeSNV.vcf", package="gQTLstats") require("VariantAnnotation") require("snpStats") vv = readVcf(fn, genome="hg19") # only 4th SNP will have dosage coding mixedVCFtoSnpMatrix(vv)$genotypes@.Data