get_dbs_context: Get DBS context

In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

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)

MutationalPatterns documentation built on Nov. 14, 2020, 2:03 a.m.