DpeakData-class: Class "DpeakData"

In 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.

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

dpeak documentation built on Nov. 8, 2020, 7:45 p.m.