Example Illumina Infinium Methylation data in MethyLumiM class

Description

An example Illumina Infinium Methylation27k dataset, which includes a control and treatment dataset with both technique and biological replicates

Usage

data(example.lumiMethy)

Details

The example dataset includes four control and four treatment samples together with their technique replicates. The original samples and technique replicates were measured in two batches. Here are the names of sixteen samples: Treat1, Treat2, Treat3, Treat4, Ctrl1, Ctrl2, Ctrl3, Ctrl4, Treat1.rep, Treat2.rep, Treat3.rep, Treat4.rep, Ctrl1.rep, Ctrl2.rep, Ctrl3.rep, Ctrl4.rep.

To save storage space, we randomly subset 5000 CpG sites among about 27000 measured CpG sites.

Examples

data(example.lumiMethy)
sampleNames(example.lumiMethy)

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.
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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(lumi)
Loading required package: Biobase
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

Welcome to Bioconductor

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

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumi/example.lumiMethy.Rd_%03d_medium.png", width=480, height=480)
> ### Name: example.lumiMethy
> ### Title: Example Illumina Infinium Methylation data in MethyLumiM class
> ### Aliases: example.lumiMethy
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(example.lumiMethy)
> sampleNames(example.lumiMethy)
 [1] "Treat1"     "Treat2"     "Treat3"     "Treat4"     "Ctrl1"     
 [6] "Ctrl2"      "Ctrl3"      "Ctrl4"      "Treat1.rep" "Treat2.rep"
[11] "Treat3.rep" "Treat4.rep" "Ctrl1.rep"  "Ctrl2.rep"  "Ctrl3.rep" 
[16] "Ctrl4.rep" 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>