convert_sigs_to_ref: Convert tissue specific signature exposures to reference

In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

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)

MutationalPatterns documentation built on Nov. 14, 2020, 2:03 a.m.