MosaicsPeakParam-class {mosaics} | R Documentation

## Class "MosaicsPeakParam"

### Description

This class represents parameters for mosaicsPeak function.

### Objects from the Class

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

### Slots

`analysisType`:

  Object of class `"character"`, representing type of data analysis.

`signalModel`:

  Object of class `"character"`, representing signal model for peak calling.

`FDR`:

  Object of class `"numeric"`, representing specified false discovery rate.

`maxgap`:

  Object of class `"numeric"`, representing maximum gap size to combine two neighboring initial peaks.

`minsize`:

  Object of class `"numeric"`, representing minimum peak size to be remained in the final peak list.

`thres`:

  Object of class `"numeric"`, representing threshold of ChIP tag count to filter initial peaks.

`decoding`:

  Object of class `"character"`, representing deconding approach for MOSAiCS-HMM peak calling.

### Author(s)

Dongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles

### References

Kuan, PF, D Chung, G Pan, JA Thomson, R Stewart, and S Keles (2011), "A Statistical Framework for the Analysis of ChIP-Seq Data", Journal of the American Statistical Association, Vol. 106, pp. 891-903.

Chung, D, Zhang Q, and Keles S (2014), "MOSAiCS-HMM: A model-based approach for detecting regions of histone modifications from ChIP-seq data", Datta S and Nettleton D (eds.), Statistical Analysis of Next Generation Sequencing Data, Springer.

### See Also

`mosaicsPeak`, `mosaicsPeakHMM`, `MosaicsPeak`.

### Examples

    showClass("MosaicsPeakParam")

[Package mosaics version 2.20.0 Index]