Description Usage Arguments Details Value See Also Examples

Tabulate somatic motifs by a grouping variable.

1 | ```
motifMatrix(vr, group = "sampleNames", normalize = TRUE)
``` |

`vr` |
GRanges object [required] |

`group` |
Grouping variable name [character, default: 'sampleNames'] |

`normalize` |
Normalize to frequency |

The 'motifMatrix' function transforms the metadata columns of a 'VRanges' object, as returned by the 'mutationContext' function, to a matrix of the form 'motifs x groups'. This constitutes the bases for the estimation of the signatures. By default (with 'normalize' set to TRUE), the counts are transformed to frequencies, such that the sum of frequencies of each group equal 1. Otherwise (with 'normalize' set to FALSE), the counts for each mofis in a group is returned.

Occurance matrix with motifs in rows and samples in columns.

'mutationContext', 'mutationContextMutect'

1 2 3 | ```
data(sca_motifs_tiny)
motifMatrix(sca_motifs_tiny, group = "study")
``` |

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

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