vcf2sm: generate a SnpMatrix instance on the basis of a VCF (4.0)...

In GGtools: software and data for analyses in genetics of gene expression

Description

generate a SnpMatrix instance on the basis of a VCF (4.0) file.

Usage

vcf2sm(tbxfi, ..., gr, nmetacol)

Arguments

tbxfi	instance of TabixFile-class
...	not used
gr	instance of GRanges-class
nmetacol	numeric: tells number of columns used in each record as locus-level metadata

Details

This function is relevant only for diallelic SNP. If any base call is denoted ‘.’, the associated genotype is set to missing (raw 0), even if the nonmissing call is ALT, implying at least one ALT.

Value

an instance of SnpMatrix-class

Author(s)

VJ Carey <[e-mail]>

References

http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf4.0

Examples

# SRC: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_07/exon/CEU.exon.2010_03.genotypes.vcf.gz
 vref = system.file("vcf/CEU.exon.2010_09.genotypes.vcf.gz", package="GGtools")
 gg = GenomicRanges::GRanges(seqnames="1", IRanges::IRanges(10e6,20e6))
 vcf2sm(Rsamtools::TabixFile(vref), gr=gg, nmetacol=9L)

GGtools documentation built on Nov. 8, 2020, 6:32 p.m.