plotInterquantileWidth: Plotting distribution of interquantile width

Description

Creates PDF file with histograms showing distribution of interquantile width of tag clusters or consensus clusters in each CAGE dataset.

Usage

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

Arguments

object

A CAGEset object

clusters

Which clusters should be used. Can be either "tagClusters" to plot distribution of interquantile width of tag clusters or "consensusClusters" to plot distribution of interquantile width of consensus clusters.

tpmThreshold

Only clusters with normalized signal >= tpmThreshold will be included in the histogram.

qLow

Position of which "lower" quantile should be used as 5' boundary. See Details.

qUp

Position of which "upper" quantile should be used as 3' boundary. See Details.

xlim

The x axis limits of the plot.

...

Additional arguments passed to plot() function, such as ylim, etc..

Value

Creates PDF file named "tagClusters_interquantile_width_all_samples.pdf" or "consensusClusters_interquantile_width_all_samples.pdf" in the working directory (depending on the value of cluster parameter). The file contains histograms showing distribution of interquantile width in every CAGE experiment.

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.

Examples

Run this code

load(system.file("data", "exampleCAGEset.RData", package="CAGEr"))

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