split_muts_region {MutationalPatterns} | R Documentation

## 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)

[Package MutationalPatterns version 3.0.1 Index]