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Last data update: 2014.03.03

R: Plot the Illumina Infinium methylation color bias in terms of...

boxplotColorBias

R Documentation

Plot the Illumina Infinium methylation color bias in terms of boxplot

Description

Plot the Illumina Infinium methylation color bias in terms of boxplot. boxplot of red and green color channel will be plotted side by side

Usage

boxplotColorBias(methyLumiM, logMode = TRUE, channel = c("both", "unmethy", "methy", "sum"), grid = TRUE, main = NULL, mar = NULL, verbose = F, subset = NULL, ...)

Arguments

`methyLumiM`	MethyLumiM-class object or eSet-class object, which include methylated and unmethylated probe intensities
`logMode`	whether plot the intensities in log-scale
`channel`	estimate the intensity in different methods
`grid`	whether to add grid on the plot
`main`	title of the plot
`mar`	margin of the plot
`verbose`	whether print verbose information during plot
`subset`	plot subset of randomly selected rows. All data will be plotted if it is NULL.
`...`	other parameters of `boxplot`

Details

Plot the Illumina Infinium methylation color bias in terms of boxplot. boxplot of red and green color channel will be plotted side by side

Value

Invisibly return TRUE if plot successfully.

Author(s)

Pan DU

Examples

data(example.lumiMethy)
boxplotColorBias(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.
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(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/boxplotColorBias.Rd_%03d_medium.png", width=480, height=480)
> ### Name: boxplotColorBias
> ### Title: Plot the Illumina Infinium methylation color bias in terms of
> ###   boxplot
> ### Aliases: boxplotColorBias
> ### Keywords: methods hplot
> 
> ### ** Examples
> 
> data(example.lumiMethy)
> boxplotColorBias(example.lumiMethy)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>