MosaicsPeakParam-class: Class "MosaicsPeakParam"

Description Objects from the Class Slots Author(s) References See Also Examples

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

1
showClass("MosaicsPeakParam")

mosaics documentation built on May 31, 2017, 3:09 p.m.

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