boxplot of a MethyLumiM object

Description

Creating a hdr.boxplot of the M-value in a MethyLumiM object

Usage

## S4 method for signature 'MethyLumiM'
boxplot(x, main, logMode = TRUE, ...)

Arguments

Details

Because the density plot of M-values usually includes two modes, using the traditional boxplot cannot accurately represent the distribution of the data. Here we use violin plot to show the density of M-values by samples

See Also

MethyLumiM-class, panel.violin and boxplot,ExpressionSet-method

Examples

## load example data
data(example.lumiMethy)
boxplot(example.lumiMethy)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> 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/boxplot-MethyLumiM-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: boxplot,MethyLumiM-method
> ### Title: boxplot of a MethyLumiM object
> ### Aliases: boxplot,MethyLumiM-method
> ### Keywords: methods hplot
> 
> ### ** Examples
> 
> ## load example data
> data(example.lumiMethy)
> boxplot(example.lumiMethy)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>