rename_nmf_signatures: Rename NMF signatures based on previously defined signatures

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

Rename NMF signatures based on previously defined signatures

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 useful for interpretation. An extracted signature that is not similar to any previously defined signatures, is not proof of a "novel" signature. The extracted signature might be a combination of known signatures, that could not be split by NMF. This can happen when, for example, too few samples were used for the NMF.

Usage

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

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"
suffix	String. The suffix added to the name of a renamed signature. Default: "-like"

Value

A nmf_res with 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 or remove the suffix of the renamed signatures.
rename_nmf_signatures(nmf_res, signatures, suffix = "")

## 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_")

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