Rcade-class {Rcade} | R Documentation |
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.
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
.
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.
Jonathan Cairns
NA
data(RcadeSTAT1) RcadeSTAT1 x <- getChIP(RcadeSTAT1) y <- getDE(RcadeSTAT1) z <- getRcade(RcadeSTAT1) plotMM(RcadeSTAT1) plotPCA(RcadeSTAT1) library(rgl) ##required for plotBBB plotBBB(RcadeSTAT1)