dpeakFit {dpeak} | R Documentation

## Fit dPeak model

### 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)

[Package dpeak version 1.4.0 Index]