mutation_context {MutationalPatterns}R Documentation

This function has been removed. Use 'mut_context' instead.

Description

This function has been removed. Use 'mut_context' instead.

Usage

mutation_context(vcf, ref_genome)

Arguments

vcf

A GRanges object

ref_genome

The reference genome

Value

Character vector with the context of the base substitutions

See Also

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)

mut_context <- mut_context(vcfs[[1]], ref_genome)
[Package MutationalPatterns version 1.12.0 Index]