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 1.4.3 Index]