Plotting pairwise scatter plots of CAGE signal and calculating correlation between samples

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Description

Creates PNG file with scatter plots of CAGE signal for all pairs of selected samples and calculates the correlation between them.

Usage

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plotCorrelation(object, what = "CTSS", values = "raw",
				samples = "all", method = "pearson",
				tagCountThreshold = 1, applyThresholdBoth = FALSE,
				plotSize = 800)

Arguments

object

A CAGEset object

what

Which level should be used for plotting and calculating correlation. Can be either "CTSS" to use individual TSSs or "consensusClusters" to use consensus clusters, i.e. entire promoters.

values

Specifies which values will be used for plotting and calculating correlation. Can be either "raw" to use raw tag count per TSS or "normalized" to use normalized CAGE signal. Used only when what = "CTSS", otherwise ignored.

samples

Character vector of sample labels for which the scatter plots should be plotted and correlation calculated. Can be either "all" to plot and calculate pairwise correlations between all samples in a CAGEset object, or a subset of valid sample labels as returned by sampleLabels function.

method

A character string indicating which correlation coefficient should be computed. Passed to cor function. Can be one of "pearson", "spearman", or "kendall".

tagCountThreshold, applyThresholdBoth

Only TSSs with tag count >= tagCountThreshold in either one (applyThresholdBoth = FALSE) or both samples (applyThresholdBoth = TRUE) are plotted and used to calculate correlation.

plotSize

Size of the individual comparison plot in pixels - the total size of the resulting png will be length(samples) * plotSize in both dimensions.

Value

Creates PNG file named "Pairwise_tag_count_correlation.png" in the working directory. Returns a matrix of pairwise correlations between selected samples.

Author(s)

Vanja Haberle

Examples

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

plotCorrelation(object = exampleCAGEset)

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