addMotifSet: 'addMotifSet'

In MOCHA: Modeling for Single-Cell Open Chromatin Analysis

addMotifSet

Description

addMotifSet Identify motifs within your peakset.

Usage

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

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'.

Value

the modified SampleTileObj with motifs added to the metadata

Examples

## Not run: 
# 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
)

## End(Not run)

MOCHA documentation built on May 29, 2024, 2:25 a.m.