count_indel_contexts: Count indel contexts
In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Description Usage Arguments Details Value See Also Examples

Count indel contexts

1	count_indel_contexts(vcf_list)

vcf_list

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

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.

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

get_indel_context

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

## 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)