custom_fcnnls: Custom Fast Combinatorial Nonnegative Least-Square.

In dami82/mutSignatures: Decipher Mutational Signatures from Somatic Mutational Catalogs

Custom Fast Combinatorial Nonnegative Least-Square.

Description

This function contributes to solve a least square linear problem using the fast combinatorial strategy from Van Benthem et al. (2004). This implementation is similar to that included in the NMF R package by Renaud Gaujoux and Cathal Seoighe, and it is tailored to the data used in the mutational signature analysis. For more info, see: https://CRAN.R-project.org/package=NMF

Usage

custom_fcnnls(mutCounts, signatures)

Arguments

mutCounts	numeric matrix including mutation counts
signatures	numeric matrix including mutation signatures

Value

list, including: (K) a numeric matrix of estimated exposures; and (Pset) a Pset numeric matrix

Examples

x <- mutSignatures:::getTestRunArgs(testN = "custom_fcnnls")
y <- mutSignatures:::custom_fcnnls(mutCounts = x$muts, signatures = x$signs)
y$coef

dami82/mutSignatures documentation built on Jan. 24, 2023, 12:21 a.m.