plotInterquantileWidth: Plot cluster widths

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

Description

Plots histograms of the interquantile width of tag clusters or consensus clusters in each CAGE dataset.

Usage

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

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

Arguments

object	A CAGEr object
clusters	Which clusters to be used. ("tagClusters" for tag clusters or "consensusClusters" for consensus clusters.
tpmThreshold	Exclude clusters with normalized signal < tpmThreshold.
qLow, qUp	Position of which "lower" (resp. "upper") quantile should be used as 5' (resp. 3') boundary. See Details.
xlim	The x axis limits of the plot.
...	Additional arguments passed to plot() function, such as ylim, etc..

Details

Interquantile width is a width (in base-pairs) of the central part of the genomic region (bounded by the positions of specified qLow and qUp quantiles) that contains >= (qUp - qLow) * 100% of the CAGE signal. Positions of specified quantiles within each cluster have to be calculated beforehand by calling quantilePositions function. 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.

Author(s)

Vanja Haberle

See Also

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

Other CAGEr clusters functions: CTSSclusteringMethod, CTSScumulativesTagClusters, CustomConsensusClusters, aggregateTagClusters, clusterCTSS, consensusClustersDESeq2, consensusClustersGR, cumulativeCTSSdistribution, quantilePositions, tagClusters

Examples

plotInterquantileWidth( object = exampleCAGEset, clusters = "tagClusters"
                      , tpmThreshold = 50, qLow = 0.1, qUp = 0.9)

plotInterquantileWidth( exampleCAGEexp, clusters = "consensusClusters"
                      , tpmThreshold = 50, qLow = 0.1, qUp = 0.9)

CAGEr documentation built on Jan. 17, 2021, 2 a.m.