generateMatrix {signeR} | R Documentation

## count matrix and opportinity matrix generators

### Description

genCountMatrixFromVcf : generate count matrix from a VCF file.
genOpportunityFromGenome : generate opportunity matrix from a target regions set.

### Usage

        genCountMatrixFromVcf(bsgenome, vcfobj)
        genOpportunityFromGenome(bsgenome, target_regions, nsamples=1)

### Arguments

`bsgenome` | A BSgenome object, equivalent to the genome used for the variant call.
`vcfobj` | A VCF object. See VCF-class from the VariantAnnotation package.
`target_regions` | A GRanges object, describing the target region analyzed by the variant caller.
`nsamples` | Number of samples to generate the matrix, should be the same number as rows of the count matrix.

### Value

A matrix of samples x (96 features).
Each feature is a SNV change with a 3bp context.

### Examples

    library(rtracklayer)
    library(VariantAnnotation)

    # input files, variant call and target
    vcf_file <- system.file("extdata","example.vcf", package="signeR")
    bed_file <- system.file("extdata","example.bed", package="signeR")

    # BSgenome, will depend on your variant call
    library(BSgenome.Hsapiens.UCSC.hg19)

    vcfobj <- readVcf(vcf_file, "hg19")
    mut <- genCountMatrixFromVcf(BSgenome.Hsapiens.UCSC.hg19, vcfobj)

    target_regions <- import(con=bed_file, format="bed")
    opp <- genOpportunityFromGenome(BSgenome.Hsapiens.UCSC.hg19,
        target_regions, nsamples=nrow(mut))

    # see also
    vignette(package="signeR")

[Package signeR version 1.20.0 Index]