motif-functions {SomaticSignatures}

Usage

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

vr    
GRanges object [required]

But, the example from the manual shows

Examples

data(sca_motifs_tiny)

motifMatrix(sca_motifs_tiny, group = "study")

However, sca_motifs is a VRange object. So, what is the right type for motifMatrix? VRange or GRange?

Both GRanges and VRanges work as inputs for motifMatrix. Since the input to that function is in most workflows the output of the mutationContext function, it often is a VRanges that describes a set of variants. But, any object that inherits from a GRanges  is suitable, if it contains the information of alteration and context.

You can check that both work the same way by trying it out:

data(sca_motifs_tiny)
m1 = motifMatrix(sca_motifs_tiny, group = "study") ## VRanges input
m2 = motifMatrix(as(sca_motifs_tiny, "GRanges"), group = "study") ## GRanges input
identical(m1, m2) ## same output