Description Usage Arguments Details Value See Also

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

1 2 | ```
nmfDecomposition(x, r, ..., includeFit = FALSE)
pcaDecomposition(x, r, ..., includeFit = FALSE)
``` |

`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. |

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.

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.

`NMF`

package

`pcaMethods`

package

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