plotGenomicAnnot-methods: plotGenomicAnnot

In transcriptR: An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification

Description

Visualize genomic distribution of ChIP-seq peaks.

Usage

plotGenomicAnnot(object, plot.type = c("distrib", "enrich"), xlab, ylab,
  color)

## S4 method for signature 'ChipDataSet'
plotGenomicAnnot(object, plot.type = c("distrib",
  "enrich"), xlab, ylab, color)

Arguments

object	A ChipDataSet object.
plot.type	Character. One of ("distrib", "enrich"). Default: "enrich".
xlab	Character. Title of the x-axis.
ylab	Character. Title of the y-axis.
color	A character vector of length four, specifying colors for distinct genomic features (TSSs, exons, introns, intergenic regions).

Details

Genomic distribution of the peaks can be visualized in two ways, either by observing the total number of peaks overlapping given genomic feature or by looking at the enrichment levels.

Value

ggplot2 object.

Author(s)

Armen R. Karapetyan

See Also

constructCDS

Examples

### Load ChipDataSet object
data(cds)

### Plot the total number of peaks overlapping distinct genomic features
plotGenomicAnnot(object = cds, plot.type = "distrib")

### Plot enrichment of the peaks at a given genomic feature (e.g. TSS)
plotGenomicAnnot(object = cds, plot.type = "enrich")

transcriptR documentation built on Nov. 8, 2020, 8:12 p.m.