split_muts_region: Split GRangesList or GRanges based on a list of regions.

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

Split GRangesList or GRanges based on a list of regions.

Description

A GRangesList or GRanges object containing variants is split based on a list of regions. This list can be either a GRangesList or a GRanges object. The result is a GRangesList where each element contains the variants of one sample from one region. Variant that are not in any of the provided region are put in a list of 'other'.

Usage

split_muts_region(vcf_list, ranges_grl, include_other = TRUE)

Arguments

vcf_list	GRangesList or GRanges object
ranges_grl	GRangesList or GRanges object containing regions of interest
include_other	Boolean. Whether or not to include a "Other" region containing mutations that aren't in any other region.

Value

GRangesList

See Also

Other genomic_regions: bin_mutation_density(), lengthen_mut_matrix(), plot_profile_region(), plot_spectrum_region()

Examples

## Read in some existing genomic regions.
## See the 'genomic_distribution()' example for how we obtained the
## following data:
CTCF_g <- readRDS(system.file("states/CTCF_g_data.rds",
  package = "MutationalPatterns"
))
promoter_g <- readRDS(system.file("states/promoter_g_data.rds",
  package = "MutationalPatterns"
))
flanking_g <- readRDS(system.file("states/promoter_flanking_g_data.rds",
  package = "MutationalPatterns"
))

## Combine the regions into a single GRangesList
regions <- GRangesList(promoter_g, flanking_g, CTCF_g)

names(regions) <- c("Promoter", "Promoter flanking", "CTCF")

## Read in some variants.
## See the 'read_vcfs_as_granges()' example for how we obtained the
## following data:
grl <- readRDS(system.file("states/read_vcfs_as_granges_output.rds",
  package = "MutationalPatterns"
))

## Split muts based on the supplied regions
split_muts_region(grl, regions)

## Don't include muts outside of the supplied regions
split_muts_region(grl, regions, include_other = FALSE)

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