lengthen_mut_matrix: Lengthen mutation matrix

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

Lengthen mutation matrix

Description

A mutation_matrix calculated on a GRangesList or GR object modified by 'split_muts_region()', will contain a column per combination of sample and genomic region. In essence different regions are treated as different samples. This function will transform the matrix, so that these regions are instead treated as different mutation types. For example, instead of 'C[C>T]G', you might have the feature 'C[C>T]G Promoter'. The number of rows in the matrix will thus be multiplied by the number of regions. After using 'split_muts_region()', use 'mut_matrix()' to get a mut_matrix that can be used for this function. The result can be plotted with plot_profile_region, but could also be used for NMF, refitting ect.

Usage

lengthen_mut_matrix(mut_matrix)

Arguments

mut_matrix

Mutation matrix

Value

mut_matrix

See Also

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

Examples

## See the 'split_muts_region()' and 'mut_matrix()' examples for how we obtained the
## mutation matrix information:
mut_mat_split_region <- readRDS(system.file("states/mut_mat_data.rds",
  package = "MutationalPatterns"
))

long_mut_mat <- lengthen_mut_matrix(mut_mat_split_region)


## This also works on indels:
## See the 'split_muts_region()' and 'count_indels_context()' examples for how we
## obtained the indel counts:
indel_counts_split <- readRDS(system.file("states/blood_indels_counts_split_region.rds",
  package = "MutationalPatterns"
))


## Lengthen the matrix
lengthen_mut_matrix(indel_counts_split)

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