QPforSig: QPforSig (internal function)

In rmpiro/decompTumor2Sig: Decomposition of individual tumors into mutational signatures by signature refitting

QPforSig (internal function)

Description

Perform quadratic programming for signatures to determine exposures.

Usage

QPforSig(counts, signatures, constrainToMaxContribution=FALSE,
tolerance=0.1)

Arguments

counts	The genome's mutation frequencies (either in Alexandrov or Shiraishi format).
signatures	The signatures to be used for decomposition. Must be in the same format as the genome's counts.
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

The decomposition in form of an exposure vector (same order as signatures).

Author(s)

Rosario M. Piro, Politecnico di Milano
Sandra Krueger, Freie Universitaet Berlin
Maintainer: Rosario M. Piro
E-Mail: <[e-mail]> or <[e-mail]>

References

http://rmpiro.net/decompTumor2Sig/
Krueger, Piro (2019) decompTumor2Sig: Identification of mutational signatures active in individual tumors. BMC Bioinformatics 20(Suppl 4):152.

rmpiro/decompTumor2Sig documentation built on May 15, 2022, 3:27 a.m.