simplifySignatures {mutSignatures}

Simplify Mutational Signatures.

Description

This function is useufl when working with non-standard muation types, such as tetra-nnucleotide mutation types or mutation types with long/complex context. THe goal of this function is to aggregated together mutations that can be simplified because of a common mutation core. For example, mutation types AA[A>T]A, TA[A>T]A, CA[A>T]A, and GA[A>T]A can be simplified to the core tri-nucleotide mutation A[A>T]A. THis function identifies mergeable mutation types, and aggregates the corresponding counts/freqs.

Usage

simplifySignatures(x, asMutationSignatures = TRUE)

Arguments

x

a mutationSignatures-class object

asMutationSignatures

logical, shall the results be returned as a mutationSignatures-class object

Details

This function is part of the user-interface set of tools included in mutSignatures. This is an exported function.

Value

object including simplified mutational signatures data

Author(s)

Damiano Fantini, [e-mail]

References

More information and examples about mutational signature analysis can be found here:

1. GitHub Repo: https://github.com/dami82/mutSignatures/

2. More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/

3. Sci Rep paper, introducing mutS: https://www.nature.com/articles/s41598-020-75062-0/

4. Oncogene paper, Mutational Signatures Operative in Bladder Cancer: https://www.nature.com/articles/s41388-017-0099-6

Examples

A <- data.frame(Sig1=1:5, Sig2=5:1, Sig3=1:5)
A <- A/apply(A, 2, sum)
rownames(A) <- c("AA[C>A]A", "CA[C>A]A", "TA[C>A]A", "TA[C>G]A", "A[C>G]AT")
A <- mutSignatures::as.mutation.signatures(A)
mutSignatures::simplifySignatures(x = A)