MOCHA (version 1.1.0)

exportMotifs: 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
)

Value

outList A List of output filepaths

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.

Examples

if (FALSE) {
MOCHA::exportMotifs(
  SampleTileObject = SampleTileMatrices,
  motifsGRanges,
  motifSetName = "CISBP",
  filterByOpenTiles = FALSE,
  outDir = tempdir(),
  verbose = TRUE
)
}