SignatureFit: Mutational Signatures Fit (deprecated)

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

Mutational Signatures Fit (deprecated)

Description

This function is deprecated. You can still use it, but we advise to use the function Fit instead, which provides a unified interface for basic signature fit with/without bootstrap. Fit a given set of mutational signatures into mutational catalogues to extimate the activty/exposure of each of the given signatures in the catalogues.

Usage

SignatureFit(
  cat,
  signature_data_matrix,
  method = "KLD",
  bf_method = "CosSim",
  alpha = -1,
  doRound = FALSE,
  verbose = TRUE,
  n_sa_iter = 500,
  showDeprecated = TRUE
)

Arguments

cat	catalogue matrix, patients as columns, channels as rows
signature_data_matrix	signatures, signatures as columns, channels as rows
method	KLD or NNLS or SA
bf_method	bleeding filter method, one of KLD or CosSim, only if bleeding filter is used (alpha>-1)
alpha	set alpha to -1 to avoid Bleeding Filter
doRound	round the exposures to the closest integer
verbose	use FALSE to suppress messages
n_sa_iter	set max Simulated Annealing iterations if method==SA
showDeprecated	set to FALSE to switch off the deprecated warning messsage

Value

returns the activities/exposures of the signatures in the given sample

Examples

res.exp <- SignatureFit(catalogues,signature_data_matrix)

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.