count_dbs_contexts: Count DBS contexts

In UMCUGenetics/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Count DBS contexts

Description

Count DBS contexts

Usage

count_dbs_contexts(vcf_list)

Arguments

vcf_list

GRanges or GRangesList object containing DBS mutations in which the context was added with get_dbs_context.

Details

Counts the number of DBS per COSMIC context from a GRanges or GRangesList object containing DBS variants. This function applies the count_dbs_contexts_gr function to each gr in its input. It then combines the results in a single tibble and returns this.

Value

A tibble containing the number of DBS per COSMIC context per gr.

See Also

get_dbs_context

Other DBS: get_dbs_context(), plot_compare_dbs(), plot_dbs_contexts(), plot_main_dbs_contexts()

Examples

## Get a GRangesList or GRanges object with DBS contexts.
## See 'dbs_get_context' for more info on how to do this.
grl_dbs_context <- readRDS(system.file("states/blood_grl_dbs_context.rds",
  package = "MutationalPatterns"
))

# Count the DBS contexts
count_dbs_contexts(grl_dbs_context)

UMCUGenetics/MutationalPatterns documentation built on Nov. 24, 2022, 4:31 a.m.