MOCHA (version 1.1.0)

addMotifSet: addMotifSet

Description

addMotifSet Identify motifs within your peakset.

Usage

addMotifSet(
  SampleTileObj,
  motifPWMs,
  w = 7,
  returnSTM = TRUE,
  motifSetName = "Motifs"
)

Value

the modified SampleTileObj with motifs added to the metadata

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
)
}