DpeakData-class {dpeak} | R Documentation

## Class "DpeakData"

### Description

This class represents dPeak data.

### Objects from the Class

Objects can be created by calls of the form `new("DpeakData", ...)`.

### Slots

`fragSet`:

  Object of class `"list"`, representing list of fragments for each peak.

`PET`:

  Object of class `"logical"`, representing whether it is paired-end tag (PET) or single-end tag (SET) data.

`fragLenTable`:

  Object of class `"table"`, representing distribution of fragment length when `PET=TRUE`.

`aveFragLen`:

  Object of class `"numeric"`, representing average fragment length when `PET=FALSE`.

`Fratio`:

  Object of class `"numeric"`, representing proportion of forward reads when `PET=FALSE`.

`stackedFragment`:

  Object of class `"list"`, representing number of fragments aligning to each genomic position.

`peakChr`:

  Object of class `"character"`, representing a vector of chromosome of each peak.

`peakStart`:

  Object of class `"numeric"`, representing a vector of start position of each peak.

`peakEnd`:

  Object of class `"numeric"`, representing a vector of end position of each peak.

`emptyList`:

  Object of class `"character"`, representing a vector of peak regions without reads.

### Methods

dpeakFit

  `signature(object = "DpeakData")`: fit the deconvolution model.

exportPlot

  `signature(x = "BinData", y = "missing", filename=NULL, strand=FALSE, extension=1, smoothing=FALSE )`: provide exploratory plots of fragments or reads in each peak region. Plots are exported to a PDF file (its file name is specified in `filename`). Options `strand`, `extension`, and `smoothing` are supported only for SET data. If `strand=TRUE`, reads are plotted in a strand-specific manner, where reads are extended to `extension` from its 5' end. If `smoothing=TRUE`, a smoothed plot (using the smoothing spline) is provided. If `strand=FALSE`, strand information is ignored.

printEmpty

  `signature(x = "DpeakData")`: provide the data frame of peak regions without reads.

show

  `signature(object = "DpeakData")`: provide brief summary of the object.

### Author(s)

Dongjun Chung

### See Also

`dpeakRead`, `dpeakFit`.

### Examples

    data(exampleData)
    exampleData

[Package dpeak version 1.2.0 Index]