plotTransform {ChIPSeqSpike} | R Documentation

## Plots average profiles of steps of the spike-in normalization

### 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)

[Package ChIPSeqSpike version 1.4.0 Index]