Rcade-class {Rcade} | R Documentation

## Rcade Class

### Description

The main class in Rcade. This class contains data pertaining to any relevant DE experiments, ChIP-seq experiments, and Rcade output from linking the previous two.

Objects of this class are typically created with the `RcadeAnalysis` function.

### Plotting methods

  `plotPCA(x, ...)`: Perform PCA analysis on the ChIP-seq data and plot the results.

  `plotMM(x, DE.abs=FALSE, ...)`: Plot ChIP log-ratios against DE log-ratios. If `DE.abs=TRUE`, then absolute values of DE log-ratios are plotted. `...` arguments are passed to `plot`.

  `plotBB(x, ...)`: Plot ChIP log-odds against DE log-odds. `...` arguments are passed to `plot`.

  `plotBBB(x, ...)`: (NB: Requires the CRAN package rgl.) 3D plot comparing log-odds values for ChIP, DE and combined ChIP & DE. `...` arguments are passed to `plot`.

### Accessors

  `getDE(x, what="summary")`: Get DE information. `what` can be: `"summary"` for the DE analysis, `"prior"` for the prior probability/probabilities of DE presence.

  `getChIP(x, what="summary")`: Get ChIP analysis information. `what` can be: `"summary"` for the analysis, `"counts"` for the raw counts, `"annoZones"` for the bins used in the analysis, `"prior"` for the prior probability/probabilities of ChIP signal presence, or `"targets"` for the targets file.

  `getRcade(x)`: Get the Rcade table - i.e. combined DE/ChIP information.

### Author(s)

Jonathan Cairns

### References

NA

### See Also

`RcadeAnalysis`

### Examples

    	data(RcadeSTAT1)
    	RcadeSTAT1

    	x <- getChIP(RcadeSTAT1)
    	y <- getDE(RcadeSTAT1)
    	z <- getRcade(RcadeSTAT1)

    	plotMM(RcadeSTAT1)
    	plotPCA(RcadeSTAT1)
    	library(rgl) ##required for plotBBB
    	plotBBB(RcadeSTAT1)

[Package Rcade version 1.24.0 Index]