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
dat
An RGChannelSet, a MethylSet or a
matrix. We either use the getBeta function to get
Beta values (for the first two) or we assume the matrix contains
Beta values.
sampGroups
Optional sample group labels. See details.
sampNames
Optional sample names. See details.
main
Plot title.
pal
Color palette.
numPositions
The density calculation uses numPositions
randomly selected CpG positions. If NULL use all positions.
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.
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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> 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
>