convert_sigs_to_ref: Convert tissue specific signature exposures to reference

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

Convert tissue specific signature exposures to reference

Description

This function converts tissue specific signature contributions into reference signature contributions. This works on SNV signatures from SIGNAL. It uses a conversion matrix to do the conversion. The output can include possible artifact signatures.

Usage

convert_sigs_to_ref(fit_res)

Arguments

fit_res

Named list with signature contributions and reconstructed mutation matrix

Value

The input fit_res, but with converted signature contributions.

Examples

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

## Get tissue specific signatures
signatures <- get_known_signatures(source = "SIGNAL", sig_type = "tissue", tissue_type = "Skin")

## Fit tissue specific signatures
fit_res <- fit_to_signatures(mut_mat, signatures)

## Convert the tissue specific signatures exposures to reference
fit_res <- convert_sigs_to_ref(fit_res)

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