exportSignals {NADfinder} | R Documentation |
Output signals to bedgraph, bed, wig, etc, for track viewer
exportSignals(dat, assayName, colName, con, format = "bedGraph", ...)
dat |
An object of GRanges, or RangedSummarizedExperiment with assays of raw counts, ratios, background correct ratios, smoothed ratios and z-scores. It should be an element of output of smoothRatiosByChromosome |
assayName |
character(1). Assay name for RangedSummarizedExperiment |
colName |
character(1). Column name of metadata of dat or assay of dat for coverage weight, see coverage, RangedSummarizedExperiment. |
con |
The connection to which data is saved. If this is a character vector, it is assumed to be a filename and a corresponding file connection is created and then closed after exporting the object. If missing, a SimpleRleList will be returned. |
format |
The format of the output. see export. |
... |
Parameters to be passed to export |
If con is missing, a SimpleRleList will be returned. Otherwise, nothing is returned.
gr <- GRanges("chr1", IRanges(seq_len(100), 201:300), reads=rep(1, 100)) myTrackLine <- new("TrackLine", name="my track", description="description of my track", color=col2rgb("red")[, 1], visibility="full") exportSignals(gr, colName="reads", con="test.bedGraph", trackLine=myTrackLine) data(triplicate.count) exportSignals(triplicate.count, "counts", "G18.subsampled.srt.bam", "test.bw", format="bigWig")