plotTransform: Plots average profiles of steps of the spike-in normalization

Description Usage Arguments Details Value Methods (by class) Author(s) See Also Examples

Description

For each experiment, plots average profiles of RPM scaled, input subtracted, RPM reversed and spiked data at different annotation locations (not available in boost mode)

Usage

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  plotTransform(theObject, legends = FALSE, colVec = NULL, 
                separateWindows = FALSE)

## S4 method for signature 'ChIPSeqSpikeDataset'
plotTransform(theObject, legends = FALSE, 
colVec = NULL, separateWindows = FALSE)

## S4 method for signature 'ChIPSeqSpikeDatasetList'
plotTransform(theObject, legends = FALSE, 
colVec = NULL, separateWindows = FALSE)

Arguments

theObject

A ChIPSeqSpikeDatasetList or ChIPSeqSpikeDataset object

legends

Logical indicating if legend should be indicated. Default is FALSE.

colVec

Character vector indicating the colors to use. Default is NULL

separateWindows

Plot each experiment in a separate window. Default is FALSE.

Details

plotTransform plots average signal over annotations that were given to the 'extractBinding' method. plotTransform is using the 'plotAverage' method of the 'seqplots' package.

The signal is plotted at four different annotation locations: 'start', 'end', 'midpoint' and 'composite' (pf, ef, mf and af options of 'plotAverage' method).

As objects created in boost mode only hold the binding values in GRanges objects, the previously applied transformations are not kept in memory. Therefore, this method does not work with ChIPSeqSpikeDatasetBoost and ChIPSeqSpikeDatasetListBoost objects.

Value

Nothing

Methods (by class)

Author(s)

Nicolas Descostes

See Also

spikeDataset extractBinding plotAverage plotProfile boxplotSpike plotHeatmaps plotCor

Examples

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data("result_extractBinding")
plotTransform(csds, TRUE)
plotTransform(csds, TRUE, separateWindows=TRUE)

descostesn/ChIPSeqSpike documentation built on Aug. 6, 2019, 3:51 p.m.