Class "TagData"

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Description

This class represents read-level ChIP-seq data.

Objects from the Class

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

Slots

coverage:

Object of class "list", a list of read coverage, where each element is a list including ChIP and matched control samples.

numReads:

Object of class "numeric", a matrix of number of reads in peak regions, where rows correspond to peak regions and columns correspond to ChIP and matched control samples.

read:

Object of class "list", a list of read-level data, where each element is a list including ChIP and matched control samples.

keepReads:

Object of class "logical", representing whether to keep read-level data.

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, extractReads, findSummit, filterPeak, MosaicsPeak.

Examples

1
showClass("TagData")