exportSignals: Output signals for visualization

In jianhong/NADfinder: Call wide peaks for sequencing data

Output signals for visualization

Description

Output signals to bedgraph, bed, wig, etc, for track viewer

Usage

exportSignals(dat, assayName, colName, con, format = "bedGraph", ...)

Arguments

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

Value

If con is missing, a SimpleRleList will be returned. Otherwise, nothing is returned.

Examples

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")

jianhong/NADfinder documentation built on Oct. 29, 2023, 11:08 a.m.