computeExplainedVariance: Compute the explained variance.

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

Description

'computeExplainedVariance()' computes for one or more tumors the variance which is explained by the estimated contributions (exposures) of a set of signatures when compared to the observed genomes.

Usage

computeExplainedVariance(exposures, signatures, genomes)

Arguments

exposures	(Mandatory) A single vector or list of vectors containing the estimated signature contributions/exposures as provided by the function decomposeTumorGenomes. A list of vectors is used if the explained variance shall be computed for multiple genomes. The number of exposure vectors must correspond to the number of genomes. The number of elements of each exposure vector must correspond to the number of signatures.
signatures	(Mandatory) The list of signatures (vectors, data frames or matrices) for which the exposures were obtained. Each of the list objects represents one mutational signature. Vectors are used for Alexandrov signatures, data frames or matrices for Shiraishi signatures.
genomes	(Mandatory) Can be either a vector, a data frame or a matrix (for an individual tumor genome), or a list of one of these object types (for multiple tumors). Each tumor genome must be of the same form as the signatures.

Value

A numeric vector of explained variances, one for each genome.

Author(s)

Rosario M. Piro
Politecnico di Milano
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.

See Also

decompTumor2Sig
decomposeTumorGenomes
plotExplainedVariance

Examples

### get Alexandrov signatures from COSMIC
signatures <- readAlexandrovSignatures()

### load preprocessed breast cancer genomes (object 'genomes') from
### Nik-Zainal et al (PMID: 22608084) 
gfile <- system.file("extdata",
         "Nik-Zainal_PMID_22608084-genomes-Alexandrov_3bases.Rdata", 
         package="decompTumor2Sig")
load(gfile)

### compute exposures
exposures <- decomposeTumorGenomes(genomes, signatures, verbose=FALSE)

### compute explained variance for the tumor genomes
computeExplainedVariance(exposures, signatures, genomes)

decompTumor2Sig documentation built on Nov. 8, 2020, 8:23 p.m.