plotProfile {ChIPSeqSpike} | R Documentation

## Plots average profiles of ChIP-seq experiments

### 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)

[Package ChIPSeqSpike version 1.10.0 Index]