fetch_cosmic_data: Fetch COSMIC mutational signatures (DEPRECATED)

In kgori/sigfit: Flexible Bayesian inference of mutational signatures

Description

fetch_cosmic_data downloads the latest release of signatures from COSMIC (http://cancer.sanger.ac.uk/cosmic/signatures) and produces a matrix of signatures that can be used for signature fitting. NB. This function is deprecated. COSMIC signatures are also provided within sigfit; for a list of available data sets, type data(package="sigfit").

Usage

fetch_cosmic_data(reorder = TRUE, remove_zeros = TRUE)

Arguments

reorder	Logical; if TRUE (default), the matrix will be reordered by substitution type and trinucleotide.
remove_zeros	Logical; if TRUE (default), pseudocounts will be added to prevent the signatures from containing any zeros, which can affect computation of the log likelihood.

Value

Matrix of signatures, with one row per signature and one column for each of the 96 trinucleotide mutation types.

kgori/sigfit documentation built on Feb. 3, 2022, 12:04 p.m.