trackCTSS: Create Genome Browser track of CTSSs.

In MalteThodberg/CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

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 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

MalteThodberg/CAGEfightR documentation built on Sept. 11, 2021, 4:42 a.m.