Last data update: 2014.03.03

R: Class "XhybExamples"
XhybExamples-classR Documentation

Class "XhybExamples"

Description

Class containing information of cross-hybridisation examples

Objects from the Class

Objects can be created by calls of the form new("XhybExamples", ...).

Slots

X:

Object of class "character" contains the ID of probe set X

Y:

Object of class "character" contains the ID of probe set Y

IVX:

Object of class "numeric" contains the expression intensities of X in the Tissue dataset

IVY:

Object of class "numeric" contains the expression intensities of Y in the Tissue dataset

IVXi:

Object of class "matrix" contains the expression intensities of X's reporters in the Tissue dataset

ai:

Object of class "numeric" contains the alignment scores of X's reporters to Y's transcript sequence

Methods

plotExample

signature(ex = "XhybExamples"): ...

Author(s)

Tineke Casneuf tine@ebi.ac.uk

References

Casneuf, Van de Peer and Huber (submitted); AtgenExpress data used: Schmid, M., Davison, T. S., Henz, S. R., Pape, U. J., Demar, M., Vingron, M. Schoelkopf, B. Weigel, D., and Lohmann, J. (2005) A gene expression map of Arabidopsis development. Nature Genetics, 37, 501-506.

Examples

data(ex1)
data(ex2)
data(ex3)
plotExample(ex1)
plotExample(ex2)
plotExample(ex3)

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(XhybCasneuf)
Loading required package: affy
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: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ath1121501cdf

Loading required package: tinesath1cdf

Attaching package: 'tinesath1cdf'

The following objects are masked from 'package:ath1121501cdf':

    i2xy, xy2i

Loading required package: RColorBrewer
Loading required package: grid
Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'ath1121501cdf' 
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'ath1121501cdf' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/XhybCasneuf/XhybExamples-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: XhybExamples-class
> ### Title: Class "XhybExamples"
> ### Aliases: XhybExamples-class plotExample plotExample,XhybExamples-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> data(ex1)
> data(ex2)
> data(ex3)
> plotExample(ex1)
> plotExample(ex2)
> plotExample(ex3)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>