addMotifSet
Identify motifs within your peakset.
Arguments
- SampleTileObj
A SummarizedExperiment, specifically the output of getSampleTileMatrix
- motifPWMs
A pwms object for the motif database. Either PFMatrix, PFMatrixList, PWMatrix, or PWMatrixList
- w
Parameter for motifmatchr controlling size in basepairs of window for filtration. Default is 7.
- returnSTM
If TRUE, return the modified SampleTileObj with motif set added to metadata (default). If FALSE, return the motifs from motifmatchr as a GRanges.
- motifSetName
Name to give motifList in the SampleTileObj's metadata if `returnSTM=TRUE`. Default is 'Motifs'.
Examples
if (FALSE) {
# load a curated motif set from library(chromVARmotifs)
# included with ArchR installation
data(human_pwms_v2)
SE_with_motifs <- addMotifSet(
SampleTileObj,
motifPWMs = human_pwms_v2,
returnSTM = TRUE, motifSetName = "Motifs", w = 7
)
}