decomposition-functions: Decomposition Functions for Somatic Signatures

In SomaticSignatures: Somatic Signatures

Description

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

Usage

  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:

• wMatrix of the form 'motif x signature'

• hMatrix of the form 'sample x signature'

• vMatrix of the form 'motif x sample', containing the reconstruction of 'm' from 'w' and 'h'.

• mInput matrix 'm'

• rNumber of signatures.

• fitFit object returned by the low-level decomposition function, if 'includeFit' is true.

See Also

NMF package

pcaMethods package

prcomp

SomaticSignatures documentation built on Nov. 8, 2020, 5:52 p.m.