gQTLseq (version 0.0.10)

vcf2sm.gr1: create a SnpMatrix instance from a VCF file, for a single GRange

Description

create a SnpMatrix instance from a VCF file, for a single GRange

Usage

vcf2sm.gr1(fn, gr, idsToKeep = NULL, nmetacol = 9L, fixDot = TRUE)

Arguments

fn

path to VCF; all TabixFile handling done internally as it is a two-pass process

gr

GRanges of length 1

idsToKeep

optional vector of sample ids that should be present and to which extract will be limited

nmetacol

what columns of the VCF record stream are feature metadata as opposed to sample variant data

fixDot

logical: if TRUE, when the locus name is ".", a chr:position name will be created and used

Value

• a RichSnpMatrix-class instance

Details

some 'esv*' tokens are repeated as feature names. these and any other duplicated names will be modified using make.unique

Examples

t17 = tiling("chr17", 10000)
GenomicRanges::seqlevels(t17) = "17"
v17 = system.file("vcf/lit17a.vcf.gz", package="chan1kg")
lapply(1:2, function(x) vcf2sm.gr1(v17, t17[x]))