dpeak-package {dpeak} | R Documentation

## dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

### Description

This package provides functions for fitting dPeak, a statistical framework to deconvolve ChIP-seq peaks.

### Details

Package: | dpeak
Type: | Package
Version: | 2.0.1
Date: | 2014-09-15
License: | GPL (>= 2)
LazyLoad: | yes

This package contains two main classes, `DpeakData` and `DpeakFit`, which represent dPeak data and deconvolution model fit, respectively. This package contains two main methods, `dpeakRead` and `dpeakFit`. `dpeakRead` method imports peak list and aligned read file and construct `DpeakData` class object. `dpeakFit` method fits deconvolution model using `DpeakData` class object and constructs `DpeakFit` class object. `DpeakFit` class object can be exported as text files and can be used for the downstream analysis.

### Author(s)

Dongjun Chung

Maintainer: Dongjun Chung <chungdon@stat.wisc.edu>

### See Also

`dpeakRead`, `dpeakFit`, `exportPeakList`, `DpeakData`, `DpeakFit`.

### Examples

    ## Not run:
    # work flow for PET data

    dataPET <- dpeakRead( peakfile="examplePeak.txt", readfile="examplePETRead.txt",
        fileFormat="eland_result", PET=TRUE )
    dataPET
    exportPlot( dataPET, filename="exPETplot.pdf" )

    fitPET <- dpeakFit( dataPET )
    fitPET
    exportPlot( fitPET, filename="exPETResult.pdf", plotType="fit" )
    exportPlot( fitPET, filename="exPETGOF.pdf", plotType="GOF" )

    # work flow for SET data

    dataSET <- dpeakRead( peakfile="examplePeak.txt", readfile="exampleSETRead.txt",
        fileFormat="eland_result", PET=FALSE, fragLen=150 )
    dataSET
    exportPlot( dataSET, filename="exSETplot_combined.pdf", strand=FALSE )
    exportPlot( dataSET, filename="exSETplot_strand_1.pdf",
        strand=TRUE, extension=1, smoothing=TRUE )
    exportPlot( dataSET, filename="exSETplot_strand_150.pdf",
        strand=TRUE, extension=150, smoothing=FALSE )

    fitSET <- dpeakFit( dataSET )
    fitSET
    exportPlot( fitSET, filename="exSETResult_combined.pdf",
        plotType="fit", strand=FALSE )
    exportPlot( fitSET, filename="exSETResult_strand_1.pdf",
        plotType="fit", strand=TRUE, extension=1, smoothing=TRUE )
    exportPlot( fitSET, filename="exSETResult_strand_150.pdf",
        plotType="fit", strand=TRUE, extension=150, smoothing=FALSE )
    exportPlot( fitSET, filename="exSETGOF.pdf", plotType="GOF" )

    # (common for both PET and SET data)

    exportPeakList( fitSET, type="txt", filename="result.txt" )
    exportPeakList( fitSET, type="bed", filename="result.bed" )
    exportPeakList( fitSET, type="gff", filename="result.gff" )

    ## End(Not run)

[Package dpeak version 1.4.0 Index]