plotInterquantileWidth: Plot cluster widths

In charles-plessy/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Plot cluster widths

Description

Histograms of the interquantile width of tag clusters or consensus clusters in each CAGE experiment.

Usage

plotInterquantileWidth(
  object,
  clusters = c("tagClusters", "consensusClusters"),
  tpmThreshold = 5,
  qLow = 0.1,
  qUp = 0.9,
  xlim = c(0, 150)
)

## S4 method for signature 'CAGEexp'
plotInterquantileWidth(
  object,
  clusters = c("tagClusters", "consensusClusters"),
  tpmThreshold = 5,
  qLow = 0.1,
  qUp = 0.9,
  xlim = c(0, 150)
)

Arguments

object	A CAGEexp object
clusters	tagClusters or consensusClusters.
tpmThreshold	Exclude clusters with normalized signal lower than tpmThreshold.
qLow, qUp	Quantile defining the 5' ("lower") and 3' ("upper") boundaries of the clusters.
xlim	Range of width to be plotted.

Details

Interquantile width is a more robust measure of the promoter width than the total span of the region, because it takes into account the magnitude of the expression in the region. Positions of specified quantiles within each cluster have to be calculated beforehand by calling quantilePositions.

Value

Plots the histograms with the ggplot2 engine and returns the plot object invisibly.

Author(s)

Vanja Haberle

Charles Plessy

See Also

Other CAGEr plot functions: hanabiPlot(), plotAnnot(), plotCorrelation(), plotExpressionProfiles(), plotReverseCumulatives()

Other CAGEr clusters functions: CTSSclusteringMethod(), CTSScumulativesTagClusters(), CustomConsensusClusters(), aggregateTagClusters(), clusterCTSS(), consensusClustersDESeq2(), consensusClustersGR(), cumulativeCTSSdistribution(), quantilePositions(), tagClustersGR()

Examples

plotInterquantileWidth( exampleCAGEexp, clusters = "tagClusters"
                      , tpmThreshold = 50, qLow = 0.1, qUp = 0.9
                      , xlim = c(2,200))
                      
plotInterquantileWidth( exampleCAGEexp, clusters = "consensusClusters"
                      , tpmThreshold = 50, qLow = 0.1, qUp = 0.9
                      , xlim = c(2,200))

charles-plessy/CAGEr documentation built on Nov. 4, 2023, 11:57 a.m.