trackClusters: Create genome browser track of clusters.

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

Description

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

Usage

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

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 Sept. 11, 2021, 4:42 a.m.