process_vcf {supersigs} | R Documentation

## Function to transform VCF object into "matrix" format

### Description

Transform a VCF object into a data frame of trinucleotide mutations with flanking bases in a wide matrix format. The function assumes that the VCF object contains only one sample and that each row in rowRanges represents an observed mutation in the sample.

### Usage

    process_vcf(vcf)

### Arguments

`vcf` | a VCF object (from `VariantAnnotation` package)

### Value

`process_vcf` returns a data frame of mutations, one row per mutation

### Examples

    # Use example vcf from VariantAnnotation
    suppressPackageStartupMessages({library(VariantAnnotation)})
    fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
    vcf <- VariantAnnotation::readVcf(fl, "hg19")

    # Subset to first sample
    vcf <- vcf[, 1]
    # Subset to row positions with homozygous or heterozygous alt
    positions <- geno(vcf)$GT != "0|0"
    vcf <- vcf[positions[, 1],]
    colData(vcf)$age <- 50        # Add patient age to colData (optional)

    # Run function
    dt <- process_vcf(vcf)
    head(dt)

[Package supersigs version 1.0.0 Index]