count_indel_contexts: Count indel contexts

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

Count indel contexts

Description

Count indel contexts

Usage

count_indel_contexts(vcf_list)

Arguments

vcf_list

GRanges or GRangesList object containing indel mutations in which the context was added with get_indel_context.

Details

Counts the number of indels per COSMIC context from a GRanges or GRangesList object containing indel mutations. This function applies the count_indel_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 indels per COSMIC context per gr.

See Also

get_indel_context

Other Indels: get_indel_context(), plot_compare_indels(), plot_indel_contexts(), plot_main_indel_contexts()

Examples

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

# Count the indel contexts
count_indel_contexts(grl_indel_context)

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