get_dbs_context {MutationalPatterns} | R Documentation

## Get DBS context

### Description

Get the DBS COSMIC context on an GRanges/GRangesList object. It applies the get_dbs_context_gr function to each gr in the input, which works by changing the REF and ALT columns of the GRanges into the COSMIC types.

### Usage

    get_dbs_context(vcf_list)

### Arguments

`vcf_list` | GRanges/GRangesList

### Value

A version of the GRanges/GRangesList object, with modified REF and ALT columns.

### See Also

`get_mut_type`, `read_vcfs_as_granges`

Other DBS: `count_dbs_contexts()`, `plot_compare_dbs()`, `plot_dbs_contexts()`, `plot_main_dbs_contexts()`

### Examples

    ## Get GRangesList with DBS.
    ## See 'get_mut_type' or 'read_vcfs_as_granges' for more info on how to do this.
    dbs_grl <- readRDS(system.file("states/blood_grl_dbs.rds",
      package = "MutationalPatterns"
    ))

    ## Set context dbs
    get_dbs_context(dbs_grl)

[Package MutationalPatterns version 3.0.1 Index]