getBestDecomp4Ksignatures {decompTumor2Sig} | R Documentation |
getBestDecomp4Ksignatures (internal function)
Description
Get the best decomposition for a subset of k signatures.
Usage
getBestDecomp4Ksignatures(genome, signatures, k,
constrainToMaxContribution=FALSE, tolerance=0.1)
Arguments
genome |
Genome for which to approximate the decomposition.
|
signatures |
The whole set of signatures (from which to choose
a subset signatures.
|
k |
Number of signatures to use (subset size).
|
constrainToMaxContribution |
(Optional) [Note: this is experimental
and is usually not needed!] If TRUE , the maximum contribution that
can be attributed to a signature will be constraint by the variant feature
counts (e.g., specific flanking bases) observed in the individual tumor
genome. If, for example, 30% of all observed variants have a specific
feature and 60% of the variants produced by a mutational process/signature
will manifest the feature, then the signature can have contributed up to
0.3/0.6 (=0.5 or 50%) of the observed variants. The lowest possible
contribution over all signature features will be taken as the allowed
maximum contribution of the signature. This allowed maximum will
additionally be increased by the value specified as tolerance
(see below). For the illustrated example and tolerance =0.1 a
contribution of up to 0.5+0.1 = 0.6 (or 60%) of the signature would be
allowed.
|
tolerance |
(Optional) If constrainToMaxContribution is
TRUE , the maximum contribution computed for a signature is increased
by this value (see above). If the parameter constrainToMaxContribution
is FALSE , the tolerance value is ignored. Default: 0.1.
|
Value
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.
Author(s)
Rosario M. Piro
Politecnico di Milano
Maintainer: Rosario
M. Piro
E-Mail: <rmpiro@gmail.com> or <rosariomichael.piro@polimi.it>
References
http://rmpiro.net/decompTumor2Sig/
Krueger, Piro (2019) decompTumor2Sig: Identification of mutational
signatures active in individual tumors. BMC Bioinformatics
20(Suppl 4):152.
[Package
decompTumor2Sig version 2.9.0
Index]