rename_nmf_signatures: Rename NMF signatures based on previously defined signatures

In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Description

This function renames signatures identified with NMF based on previously defined signatures. If a NMF signature has a cosine similarity with a previously defined signature, that is higher than the cutoff, then this NMF signature will get the name of the previously defined signature. If not the NMF signature will receive a letter based name. For example: SBSA. This only changes the names of signatures, not their actual values. This function can be help with identifying whether signatures found with NMF are already known, which can be usefull for interpretation.

Usage

rename_nmf_signatures(nmf_res, signatures, cutoff = 0.85, base_name = "SBS")

Arguments

nmf_res	Named list of mutation matrix, signatures and signature contribution
signatures	A signature matrix
cutoff	Cutoff at which signatures are considered similar. Default: 0.85
base_name	The base part of a letter based signature name. Default: "SBS"

Value

A nmf_res whith changed signature names

Examples

## Extracting signatures can be computationally intensive, so
## we use pre-computed data generated with the following command:
# nmf_res <- extract_signatures(mut_mat, rank = 2)

nmf_res <- readRDS(system.file("states/nmf_res_data.rds",
  package = "MutationalPatterns"
))

## Get signatures
signatures <- get_known_signatures()

rename_nmf_signatures(nmf_res, signatures)

## You can change how similar the signatures have to be, before they are considered similar.
rename_nmf_signatures(nmf_res, signatures, cutoff = 0.95)

## You can also change the base_name of the signatures that end up with a letter name.
rename_nmf_signatures(nmf_res, signatures, cutoff = 0.95, base_name = "Signature_")

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