mutational-signatures {SomaticSignatures} | R Documentation

## 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.

### 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)

[Package SomaticSignatures version 2.30.0 Index]