count_indel_contexts {MutationalPatterns} | R Documentation |
Count indel contexts
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.
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)