dpeakFit: Fit dPeak model

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

Description

Fit a deconvolution model.

Usage

dpeakFit( object, ... )
## S4 method for signature 'DpeakData'
dpeakFit( object, 
	objectMotif=NULL, estDeltaSigma="common", init="localmax", 
	nTop=100, lbDelta = 25, lbSigma = 25,
    psize=21, maxComp=5, pConst=0.2, nCore=1, verbose=FALSE, iterInit=50, iterMain=25, epsilon=1e-6 )

Arguments

object	Object of class DpeakData, dPeak data imported using method dpeakRead.
objectMotif	Object of class DpeakMotif, motif data generated using method dpeakMotif. If incorporated, locations of binding events are initialized using motif information.
estDeltaSigma	Approach to estimate delta and sigma parameters for SET data. Possible values are either "common" (estimate single delta and sigma parameters that are used for all peaks) or "separate" (estimate delta and sigma parameters for each peak separately). Default is "common". Not relevant when PET data is used.
init	Approach to initialize locations of binding events. Possible values are "localmax" and "uniform". Default is "localmax".
nTop	Number of candidate regions used to estimate common delta and sigma estimates. Relevant only when estDeltaSigma="common".
lbDelta	Lower bound for delta parameter.
lbSigma	Lower bound for sigma parameter.
psize	Approximate size of the binding protein of interest.
maxComp	Maximum possible number of binding events in each peak region.
pConst	Value to determine the plateau in the BIC curve. Should be a value larger than zero and smaller than one.
nCore	Number of CPUs to be used when parallel computing is utilized.
verbose	Use verbose mode? Possible values are either TRUE (use) or FALSE (do not use).
iterInit	Iteration number for initial estimation of binding sites.
iterMain	Iteration number for main estimation of binding sites.
epsilon	Criterion to stop iteration for binding site estimation.
...	Other parameters to be passed through to generic dpeakFit.

Details

Parallel computing can be utilized for faster computation if parallel package is installed. Users can change the number of CPUs to be used by changing the argument nCore.

Value

Construct DpeakFit class object.

Author(s)

Dongjun Chung

See Also

dpeakRead, DpeakFit.

Examples

data(exampleData)
exampleFit <- dpeakFit(exampleData, maxComp = 5)

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