count_mbs_contexts: Count MBS variants grouped by length.

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

Count MBS variants grouped by length.

Description

Count MBS variants grouped by length.

Usage

count_mbs_contexts(vcf_list)

Arguments

vcf_list

GRanges or GRangesList object containing mbs variants.

Details

Counts the number of mbs grouped by length from a GRanges or GRangesList object containing mbs variants. This is used, since a COSMIC context has to our knowledge not yet been defined. This function applies the count_mbs_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 MBS per MBS length per gr.

See Also

Other MBS: plot_compare_mbs(), plot_mbs_contexts()

Examples

## Get a GRangesList or GRanges object with mbs variants.
mbs_grl <- readRDS(system.file("states/blood_grl_mbs.rds",
  package = "MutationalPatterns"
))

# Count the MBSs
count_mbs_contexts(mbs_grl)

CuppenResearch/MutationalPatterns documentation built on Nov. 23, 2022, 4:13 a.m.