variantContext: Gather variant context around single nucleotide variants

In seandavi/MutationTools: What the package does (short line)

Description

The variant context is defined by gathering the nucleotides upstream and downstream of a variant. This if often the first step in building a mutation spectrum analysis.

Usage

variantContext(VARIANTS, FASTA, ...)

## S4 method for signature 'VCF,FaFile'
variantContext(VARIANTS, FASTA, ...)

## S4 method for signature 'VRanges,FaFile'
variantContext(VARIANTS, FASTA, ...)

Arguments

variants	A VCF-class object
fasta	A FaFile object that describes the fasta file location of the reference sequence
extendBy	The number of bases on either side of the altered base to capture. The altered base will be placed in the center of the context. For example, the default value of 1 will result in contexts of length 3. Specifying 2 will result in contexts of length 5, etc.

Value

A VariantContext object.

Methods (by class)

• VARIANTS = VCF,FASTA = FaFile:

• VARIANTS = VRanges,FASTA = FaFile:

Examples

library(VariantAnnotation)
fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
param <- ScanVcfParam(info=c("DP"))
vcf = readVcf(fl,"hg19",param=param)
seqlevels(vcf) = paste0('chr',seqlevels(vcf))
variantContext(vcf,fasta=FaFile('/data/CCRBioinfo/public/GATK/bundle/2.3/hg19/ucsc.hg19.fasta'))

seandavi/MutationTools documentation built on May 29, 2019, 4:32 p.m.