decomposition-signatures: Decomposition Functions for 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.
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.
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.