DpeakData-class: Class "DpeakData"

Description Objects from the Class Slots Methods Author(s) See Also Examples

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

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carter-allen/dpeak documentation built on April 23, 2020, 4:09 p.m.