trackCTSS {CAGEfightR} | R Documentation |
Create a Gviz-track of CTSSs, where Plus/minus strand signal is shown positive/negative. This representation makes it easy to identify bidirectional peaks.
trackCTSS(object, ...) ## S4 method for signature 'GRanges' trackCTSS(object, plusColor = "cornflowerblue", minusColor = "tomato", ...) ## S4 method for signature 'RangedSummarizedExperiment' trackCTSS(object, ...) ## S4 method for signature 'GPos' trackCTSS(object, ...)
object |
GenomicRanges or RangedSummarizedExperiment: Ranges with CTSSs in the score column. |
... |
additional arguments passed on to DataTrack. |
plusColor |
character: Color for plus-strand coverage. |
minusColor |
character: Color for minus-strand coverage. |
DataTrack-object.
Other Genome Browser functions:
trackBalance()
,
trackClusters()
,
trackLinks()
library(Gviz) data(exampleCTSSs) data(exampleUnidirectional) data(exampleBidirectional) # Example uni- and bidirectional clusters TC <- rowRanges(subset(exampleUnidirectional, width>=100)[3,]) BC <- rowRanges(exampleBidirectional[3,]) # Create pooled track subsetOfCTSSs <- subsetByOverlaps(rowRanges(exampleCTSSs), c(BC, TC, ignore.mcols=TRUE)) pooledTrack <- trackCTSS(subsetOfCTSSs) # Plot plotTracks(pooledTrack, from=start(TC)-100, to=end(TC)+100, chromosome=seqnames(TC), name='TC') plotTracks(pooledTrack, from=start(BC)-100, to=end(BC)+100, chromosome=seqnames(BC), name='BC') # See vignette for examples on how to combine multiple Gviz tracks