queryVCF: obtain SnpMatrix from VCF genotypes

In gQTLstats: gQTLstats: computationally efficient analysis for eQTL and allied studies

Description

obtain SnpMatrix from VCF genotypes

Usage

queryVCF(gr, vcf.tf, samps, genome = "hg19", getSM = TRUE,
   snvOnly=TRUE)

Arguments

gr	GRanges instance; SNPs lying within will be processed
vcf.tf	TabixFile instance pointing to VCF
samps	samples to be retained
genome	tag identifying build
getSM	logical; if FALSE, genotypeToSnpMatrix will not be run and only the output of readVcf is returned.
snvOnly	logical, if TRUE, will confine results to SNV

Value

a list of length two

readout	output of readVcf
sm	output of genotypeToSnpMatrix run on the read result

Examples

require(Rsamtools)
tf20 = TabixFile(system.file("vcf/c20exch.vcf.gz", package="gQTLstats"))
require(geuvPack)
data(geuFPKM)
lgeu = geuFPKM[ which(seqnames(geuFPKM)=="chr20"), 
    which(geuFPKM$popcode=="CEU") ]
seqlevelsStyle(lgeu) = "NCBI"
rng = rowRanges(lgeu)[232] # CPNE1
myq = queryVCF( rng, tf20, samps=colnames(lgeu), genome="hg19" )
myq

gQTLstats documentation built on Nov. 8, 2020, 7:53 p.m.