motif-functions {SomaticSignatures} | R Documentation

## Group somatic moticfs

### Description

Tabulate somatic motifs by a grouping variable.

### Usage

    motifMatrix(vr, group = "sampleNames", normalize = TRUE)

### Arguments

`vr` | GRanges object [required]
`group` | Grouping variable name [character, default: 'sampleNames']
`normalize` | Normalize to frequency

### Details

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.

### Value

Occurance matrix with motifs in rows and samples in columns.

### See Also

'mutationContext', 'mutationContextMutect'

### Examples

    data(sca_motifs_tiny)

    motifMatrix(sca_motifs_tiny, group = "study")

[Package SomaticSignatures version 2.16.0 Index]