mutational-signatures: Estimate Somatic Signatures

In julian-gehring/SomaticSignatures: 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.

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

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

sigs = identifySignatures(sca_mm, 5)

julian-gehring/SomaticSignatures documentation built on May 31, 2020, 5:54 a.m.