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

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)