DpeakData-class: Class "DpeakData"

In dongjunchung/dpeak: dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

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.

plot

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.

print

signature(x = "DpeakData"): (not supported yet)

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

showClass("DpeakData")
## Not run: 
# PET data

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

# SET data

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

## End(Not run)

dongjunchung/dpeak documentation built on March 1, 2020, 3:44 a.m.