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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Rcade)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: baySeq
Loading required package: abind
Loading required package: perm
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Welcome to Rcade - version 1.14.0
If you are new to Rcade, please consider reading the vignette through the command: vignette("Rcade").

Attaching package: 'Rcade'

The following object is masked from 'package:BiocGenerics':

    plotPCA

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Rcade/Rcade-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Rcade-class
> ### Title: Rcade Class
> ### Aliases: Rcade-class plotBBB plotMM plotBB plotPCA plotBBB,Rcade-method
> ###   plotMM,Rcade-method plotBB,Rcade-method plotPCA,Rcade-method getDE
> ###   getChIP getRcade getDE,Rcade-method getChIP,Rcade-method
> ###   getRcade,Rcade-method getDE<- getChIP<- getRcade<-
> ###   getDE<-,Rcade-method getChIP<-,Rcade-method getRcade<-,Rcade-method
> ### Keywords: misc
> 
> ### ** Examples
> 
> 	data(RcadeSTAT1)
> 	RcadeSTAT1
Rcade: 57 rows, 15 columns.
DE: 59 rows, 13 columns.
ChIP: 1 track(s):
[[1]]
annoZones: GRanges with 48 ranges and 1 elementMetadata col.
shift:0 
counts: 48 rows, 4 columns.
summary: 48 rows, 4 columns.

Metadata:
ChIPtargets: 4 rows, 5 columns.
fileDir:/home/cairnsj/R/x86_64-pc-linux-gnu-library/3.1/Rcade/extdata/STAT1
> 
> 	x <- getChIP(RcadeSTAT1)
> 	y <- getDE(RcadeSTAT1)
> 	z <- getRcade(RcadeSTAT1)
> 
> 	plotMM(RcadeSTAT1)
Loading required package: plotrix
> 	plotPCA(RcadeSTAT1)
> 	library(rgl) ##required for plotBBB

Attaching package: 'rgl'

The following object is masked from 'package:plotrix':

    mtext3d

> 	plotBBB(RcadeSTAT1)
Warning message:
In .local(x, ...) : Removed at least one gene with infinite B.ChIP.DE
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>