plotProfile: Plots average profiles of ChIP-seq experiments

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

Description

Plots average profiles of all experiments contained in a 'spikeDataset' at different locations

Usage

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    plotProfile(theObject, legends = FALSE, colVec = NULL, notScaled = FALSE)

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

## S4 method for signature 'ChIPSeqSpikeDatasetBoost'
plotProfile(theObject, legends = FALSE, 
colVec = NULL)

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

## S4 method for signature 'ChIPSeqSpikeDatasetListBoost'
plotProfile(theObject, legends = 
 FALSE, colVec = NULL)

Arguments

theObject

ChIPSeqSpike dataset (see ?spikeDataset)

legends

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

colVec

Character vector indicating the colors to use. Default is NULL

notScaled

If not in boost mode, logical indicating if untransformed data should be plotted. Default is FALSE.

Details

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

By default, the spiked signal is plotted. If the 'notScaled' parameter is set to TRUE and the object is of type ChIPSeqSpikeDatasetList or ChIPSeqSpikeDataset (no boost mode), the RPM scaled and input subtracted values are also plotted. This option enables to visualize the effect of spike-in scaling.

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

Value

Nothing

Methods (by class)

Author(s)

Nicolas Descostes

See Also

spikeDataset extractBinding plotAverage plotTransform boxplotSpike plotHeatmaps plotCor

Examples

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data("result_extractBinding")
plotProfile(csds)
plotProfile(csds, TRUE)
plotProfile(csds, TRUE, notScaled = TRUE)

ChIPSeqSpike documentation built on Nov. 8, 2020, 5:29 p.m.