TagData-class {mosaics} | R Documentation

## Class "TagData"

### 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

    showClass("TagData")

[Package mosaics version 2.28.0 Index]