type_context: Retrieve context of base substitution types

In UMCUGenetics/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

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, extension = 1)

Arguments

vcf	A CollapsedVCF object
ref_genome	Reference genome
extension	The number of bases, that's extracted upstream and downstream of the base substitutions. (Default: 1).

Value

Mutation types and context character vectors in a named list

See Also

read_vcfs_as_granges, mut_context

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)

## Get type context
type_context <- type_context(vcfs[[1]], ref_genome)

## Get larger type context
type_context_larger <- type_context(vcfs[[1]], ref_genome, extension = 2)

UMCUGenetics/MutationalPatterns documentation built on Nov. 24, 2022, 4:31 a.m.