trackCTSS {CAGEfightR} | R Documentation

## Create Genome Browser track of CTSSs.

### Description

Create a Gviz-track of CTSSs, where Plus/minus strand signal is shown positive/negative. This representation makes it easy to identify bidirectional peaks.

### Usage

    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, ...)

### Arguments

`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.

### Value

DataTrack-object.

### See Also

Other Genome Browser functions: `trackBalance()`, `trackClusters()`, `trackLinks()`

### Examples

    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 trakc
    subsetOfCTSSs <- subsetByOverlaps(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

[Package CAGEfightR version 1.7.5 Index]