mutational-signatures: Estimate Somatic Signatures

Description Usage Arguments Details Value See Also Examples

Description

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

Usage

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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.

Details

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

Value

An object of class 'MutationalSignatures'.

See Also

The predefined decomposition functions: nmfDecomposition and pcaDecomposition

mutationContext, mutationContextMutect

motifMatrix

MutationalSignatures class

Examples

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

sigs = identifySignatures(sca_mm, 5)

SomaticSignatures documentation built on Nov. 1, 2018, 2:23 a.m.