motif-functions: Group somatic moticfs

In SomaticSignatures: Somatic Signatures

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")

SomaticSignatures documentation built on Nov. 8, 2020, 5:52 p.m.