trackClusters: Create genome browser track of clusters.

Description Usage Arguments Value See Also Examples

Description

Create a Gviz-track of clusters (unidirectional TCs or bidirectional enhancers), where cluster strand and peak is indicated.

Usage

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trackClusters(object, ...)

## S4 method for signature 'GRanges'
trackClusters(object, plusColor = "cornflowerblue",
  minusColor = "tomato", unstrandedColor = "hotpink", ...)

## S4 method for signature 'RangedSummarizedExperiment'
trackClusters(object, ...)

Arguments

object

GRanges: GRanges with peaks in the thick-column.

...

additional arguments passed on to GeneRegionTrack.

plusColor

character: Color for plus-strand features.

minusColor

character: Color for minus-strand features.

unstrandedColor

character: Color for unstranded features.

Value

GeneRegionTrack-object.

See Also

Other Genome Browser functions: trackBalance, trackCTSS, trackLinks

Examples

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library(Gviz)
data(exampleUnidirectional)

# Find some wide unidirectional clusters:
TCs <- subset(exampleUnidirectional, width >= 100)

# Create track
clusters_track <- trackClusters(TCs[1:2,], name='Tag clusters', col=NULL)

# Plot
plotTracks(clusters_track)

# See vignette for examples on how to combine multiple Gviz tracks

MalteThodberg/CAGEfightR documentation built on May 8, 2019, 3:36 p.m.