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)