decomposition-functions: Decomposition Functions for Somatic Signatures

Description Usage Arguments Details Value See Also

Description

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

Usage

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  nmfDecomposition(x, r, ..., includeFit = FALSE)
  pcaDecomposition(x, r, ..., includeFit = FALSE)

Arguments

x

GRanges object [required]

r

Number of signatures [integer, required]

...

Additional arguments passed to 'NMF::nmf' or 'pcaMethods::pca'.

includeFit

Include the fit object returned by the low-level decomposition function in the output.

Details

The 'nmfDecomposition' and 'pcaDecomposition' functions estimate a set of 'r' somatic signatures using the NMF or PCA, respectively.

In previous versions of the package, these functions were known as 'nmfSignatures' and 'pcaSignatures', respectively. While they are still available, we recommend using the new naming convention.

Value

The 'signature' functions return a list with the elements:

See Also

NMF package

pcaMethods package

prcomp


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