mut_context {MutationalPatterns} | R Documentation

## Retrieve context of base substitutions

### Description

A function to extract the bases 3' upstream and 5' downstream of the base substitutions from the reference genome. The user an choose how many bases are extracted.

### Usage

    mut_context(vcf, ref_genome, extension = 1)

### Arguments

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

### Value

Character vector with the context of the base substitutions

### See Also

`read_vcfs_as_granges`,

### 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 the standard context
    mut_context <- mut_context(vcfs[[1]], ref_genome)

    ## Get larger context
    mut_context_larger <- mut_context(vcfs[[1]], ref_genome, extension = 2)

[Package MutationalPatterns version 3.0.1 Index]