DpeakFit-class {dpeak} | R Documentation

## Class "DpeakFit"

### Description

This class represents deconvolution model fit.

### Objects from the Class

Objects can be created by calls of the form `new("DpeakFit", ...)`.

### Slots

`fits`:

  Object of class `"list"`, representing list of deconvolution fits of all possible models for each peak.

`optFit`:

  Object of class `"list"`, representing list of fits of the optimal model for each peak.

`optMu`:

  Object of class `"list"`, representing list of binding sites of the optimal model for each peak.

`optPi`:

  Object of class `"list"`, representing list of relative strengths of the optimal model for each peak.

`optPi0`:

  Object of class `"list"`, representing list of background strengths of the optimal model for each peak.

`optGamma`:

  Object of class `"list"`, representing list of background proportion of the optimal model for each peak.

`optDelta`:

  Object of class `"list"`, representing list of read shift of the optimal model for each peak when `PET=FALSE`.

`optSigma`:

  Object of class `"list"`, representing list of read standard deviation of the optimal model for each peak when `PET=FALSE`.

`bicVec`:

  Object of class `"list"`, representing list of BIC values for each peak.

`aicVec`:

  Object of class `"list"`, representing list of AIC values for each peak.

`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.

`estDeltaSigma`:

  Object of class `"character"`, representing the approach to estimate delta and sigma parameters for SET data.

`nTop`:

  Object of class `"numeric"`, representing the number of candidate regions used to estimate common delta and sigma estimates.

`lbDelta`:

  Object of class `"numeric"`, representing a lower bound for the delta parameter.

`lbSigma`:

  Object of class `"numeric"`, representing a lower bound for the sigma parameter.

`psize`:

  Object of class `"numeric"`, representing approximate size of the binding protein of interest.

`maxComp`:

  Object of class `"numeric"`, representing maximum possible number of binding events in each peak region.

`pConst`:

  Object of class `"numeric"`, representing value to determine the plateau in the BIC curve.

`iterInit`:

  Object of class `"numeric"`, representing iteration number for initial estimation of binding sites.

`iterMain`:

  Object of class `"numeric"`, representing iteration number for main estimation of binding sites.

`epsilon`:

  Object of class `"numeric"`, representing criterion to stop iteration for binding site estimation.

### Methods

exportPlot

  `signature(x = "DpeakFit", y = "missing", filename=NULL, plotType="fit", strand=FALSE, extension=1, smoothing=FALSE, threshold=0.10, nsimul=10000, seed=12345, nCore=8)`: draw plots of deconvolution results if `plotType="fit"`, goodness of fit (GOF) plots if `plotType="GOF"`, or plots of Bayesian information criterion (BIC) and Akaike information criterion (AIC) curves if `plotType="BIC"`. Plots are exported to a PDF file (its file name is specified in `filename`). In deconvolution result plots, binding sites with strength larger than `threshold` are drawn in dark blue and other binding sites are drawn in light blue. When `plotType="fit"`, options `strand`, `extension`, and `smoothing` are supported 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. For the GOF plots, `nsimul` fragments are simulated from the fitted model (`seed` indicates random seed; `nCore` CPUs are used for parallel computing).

show

  `signature(object = "DpeakFit")`: provide brief summary of the object.

### Author(s)

Dongjun Chung

### See Also

`dpeakFit`, `exportPeakList`.

### Examples

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

[Package dpeak version 1.4.0 Index]