plotInterquantileWidth: Plotting distribution of interquantile width

In ge11232002/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

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..

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.

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.

Author(s)

Vanja Haberle

See Also

quantilePositions

Examples

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

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

ge11232002/CAGEr documentation built on May 17, 2019, 12:13 a.m.