Export motif annotations from addMotifSet()
to BigBed format for visualization in genome browsers.
Source: R/exportCoverage.R
exportMotifs.Rd
exportMotifs
exports a motif set GRanges from running
addMotifSet()
(with `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()
(with `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
)
}