plotProfile: Plots average profiles of ChIP-seq experiments

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

Description

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

Usage

    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)

• ChIPSeqSpikeDataset: Method for signature theObject= 'ChIPSeqSpikeDataset'

• ChIPSeqSpikeDatasetBoost: Method for signature theObject= 'ChIPSeqSpikeDatasetBoost'

• ChIPSeqSpikeDatasetList: Method for signature theObject= 'ChIPSeqSpikeDatasetList'

• ChIPSeqSpikeDatasetListBoost: Method for signature theObject= ChIPSeqSpikeDatasetListBoost'

Author(s)

Nicolas Descostes

See Also

spikeDataset extractBinding plotAverage plotTransform boxplotSpike plotHeatmaps plotCor

Examples

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

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