# Extract mutational signatures from trinucletide context.

### Description

Decompose a matrix of 96 substitution classes into `n`

signatures.

### Usage

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### Arguments

`mat` |
Input matrix of diemnsion nx96 generated by |

`n` |
decompose matrix into n signatures. Default NULL. Tries to predict best value for |

`nTry` |
tries upto this number of signatures before choosing best |

`plotBestFitRes` |
plots consensus heatmap for range of values tried. Default FALSE |

`parallel` |
calls to .opt argument of |

### Details

This function decomposes a non-negative matrix into n signatures. Extracted signatures are compared against 21 experimentally validated signatures by calculating cosine similarity. See http://www.nature.com/nature/journal/v500/n7463/fig_tab/nature12477_F2.html for details. Please be noted that the original study described 21 validated signatures, however cosimc catalogue of cancer signatures has now reached ~30 signatures. Validated signatures lack some of, now well known signatures such Signature-22 (T>A strand bias occuring in liver), and this comparison might not include them. In that case you may have to manually infer the results.

### Value

a list with decomposed scaled signatures, signature contributions in each sample and a cosine similarity table against validated signatures.

### See Also

`trinucleotideMatrix`

`plotSignatures`

### Examples

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