SomaticSignatures (version 2.8.4)

mutational-signatures: Estimate Somatic Signatures

Description

Estimate somatic signatures from sequence motifs with a selection of statistical methods.

Usage

identifySignatures(m, nSigs, decomposition = nmfDecomposition, ...)

Arguments

m

Motif matrix, as returned by 'motifMatrix' [required].

nSigs

Number of signatures [integer, required].

decomposition

Function to apply for the matrix decomposition. The methods NMF and PCA are already implemented in the functions 'nmfDecomposition' and 'pcaDecomposition', respectively.

...

Additional arguments passed to the 'decomposition' function.

Value

An object of class 'MutationalSignatures'.

Details

'identifySignatures' estimate a set of 'r' somatic signatures, based on a matrix decomposition method (such as NMF, PCA).

See Also

The predefined decomposition functions: nmfDecomposition and pcaDecomposition

mutationContext, mutationContextMutect

motifMatrix

MutationalSignatures class

Examples

data("sca_mm", package = "SomaticSignatures")

sigs = identifySignatures(sca_mm, 5)