exportMotifs: 'exportMotifs'

In MOCHA: Modeling for Single-Cell Open Chromatin Analysis

exportMotifs

Description

exportMotifs exports a motif set GRanges from running addMotifSet(returnSTM=FALSE) to bigBed file files for visualization in genome browsers.

Usage

exportMotifs(
  SampleTileObject,
  motifsGRanges,
  motifSetName = "motifs",
  filterByOpenTiles = FALSE,
  outDir,
  verbose = FALSE
)

Arguments

SampleTileObject	The SummarizedExperiment object output from getSampleTileMatrix
motifsGRanges	A GRanges containing motif annotations, typically from addMotifSet(returnSTM=FALSE)
motifSetName	Optional, a name indicating the motif set. Used to name files in the specified outdir. Default is "motifs".
filterByOpenTiles	Boolean. If TRUE, a bigBed file will be exported for each cell population with motifs filtered to those occurring only in open tiles.
outDir	Desired output directory where bigBed files will be saved
verbose	Set TRUE to display additional messages. Default is FALSE.

Value

outList A List of output filepaths

Examples

## Not run: 
MOCHA::exportMotifs(
  SampleTileObject = SampleTileMatrices,
  motifsGRanges,
  motifSetName = "CISBP",
  filterByOpenTiles = FALSE,
  outDir = tempdir(),
  verbose = TRUE
)

## End(Not run)

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