processMultipleSigSets {decompTumor2Sig} | R Documentation |
Performs the quadratic programming/exposure prediction for multiple
subsets (of size k) of mutational signatures and returns information on the
best subset (highest explained variance). This function is used by
getBestDecomp4Ksignatures
and addBestSignatureToSubset
.
processMultipleSigSets(genome, signatures, sigCombn, k, constrainToMaxContribution=FALSE, tolerance=0.1)
genome |
Genome for which to approximate the decomposition. |
signatures |
The whole set of signatures (from which to choose a subset signatures. |
sigCombn |
The combinations of subsets of |
k |
Number of signatures to use (subset size). |
constrainToMaxContribution |
(Optional) [Note: this is experimental
and is usually not needed!] If |
tolerance |
(Optional) If |
A list object containing: k=number of signatures; explVar=variance explained by these signatures; sigList=list of the signatures; decomposition=decomposition (exposures) obtained with these signatures.
Rosario M. Piro
Freie Universitaet Berlin
Maintainer: Rosario
M. Piro
E-Mail: <rmpiro@gmail.com> or <r.piro@fu-berlin.de>
http://rmpiro.net/decompTumor2Sig/
Krueger, Piro (2018) decompTumor2Sig: Identification of mutational
signatures active in individual tumors. BMC Bioinformatics (accepted for
publication).
Krueger, Piro (2017) Identification of Mutational Signatures Active in
Individual Tumors. NETTAB 2017 - Methods, Tools & Platforms for
Personalized Medicine in the Big Data Era, October 16-18, 2017, Palermo,
Italy. PeerJ Preprints 5:e3257v1, 2017.