R: Retrieve context of base substitution types

type_context {MutationalPatterns}

R Documentation

Retrieve context of base substitution types

Description

A function to extract the bases 3' upstream and 5' downstream of the base substitution types.

Usage

type_context(vcf, ref_genome)

Arguments

`vcf`	A CollapsedVCF object
`ref_genome`	Reference genome

Value

Mutation types and context character vectors in a named list

Examples

## See the 'read_vcfs_as_granges()' example for how we obtained the
## following data:
vcfs <- readRDS(system.file("states/read_vcfs_as_granges_output.rds",
                package="MutationalPatterns"))

## Load the corresponding reference genome.
ref_genome <- "BSgenome.Hsapiens.UCSC.hg19"
library(ref_genome, character.only = TRUE)

type_context <- type_context(vcfs[[1]], ref_genome)