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

In descostesn/ChIPSeqSpike: ChIP-Seq data scaling according to spike-in control

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

  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)

• ChIPSeqSpikeDataset: Method for signature theObject= 'ChIPSeqSpikeDataset'

• ChIPSeqSpikeDatasetList: Method for signature theObject= 'ChIPSeqSpikeDatasetList'

Author(s)

Nicolas Descostes

See Also

spikeDataset extractBinding plotAverage plotProfile boxplotSpike plotHeatmaps plotCor

Examples

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

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