Density bean plots of methylation Beta values.

Description

Density ‘bean’ plots of methylation Beta values, primarily for QC.

Usage

densityBeanPlot(dat, sampGroups = NULL, sampNames = NULL, main = NULL,
    pal = brewer.pal(8, "Dark2"), numPositions = 10000)

Arguments

Details

This function produces the density bean plot component of the QC report. If sampGroups is specified, group-specific colors will be used. For speed reasons the plots are produced using a random subset of CpG positions. The number of positions used is specified by the numPositions option.

Value

No return value. Plots are produced as a side-effect.

Author(s)

Martin Aryee aryee@jhu.edu.

References

P Kampstra. Beanplot: A boxplot alternative for visual comparison of distributions. Journal of Statistical Software 28, (2008). http://www.jstatsoft.org/v28/c01

See Also

qcReport, mdsPlot, controlStripPlot, densityPlot

Examples

if (require(minfiData)) {

names <- pData(RGsetEx)$Sample_Name
groups <- pData(RGsetEx)$Sample_Group
par(mar=c(5,6,4,2))
densityBeanPlot(RGsetEx, sampNames=names, sampGroups=groups)

}

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(minfi)
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: lattice
Loading required package: GenomicRanges
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: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/minfi/densityBeanPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: densityBeanPlot
> ### Title: Density bean plots of methylation Beta values.
> ### Aliases: densityBeanPlot
> 
> ### ** Examples
> 
> if (require(minfiData)) {
+ 
+ names <- pData(RGsetEx)$Sample_Name
+ groups <- pData(RGsetEx)$Sample_Group
+ par(mar=c(5,6,4,2))
+ densityBeanPlot(RGsetEx, sampNames=names, sampGroups=groups)
+ 
+ }
Loading required package: minfiData
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>