MosaicsPeakParam-class: Class "MosaicsPeakParam"

In mosaics: MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)

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")

mosaics documentation built on Nov. 8, 2020, 6:59 p.m.