RnBeadRawSet or RnBeadSet object with valid quality
control information.
type
type of the control probe; must be one of the "BISULFITE CONVERSION I",
"BISULFITE CONVERSION II", "EXTENSION", "HYBRIDIZATION", "NEGATIVE",
"NON-POLYMORPHIC", "NORM_A", "NORM_C", "NORM_G", "NORM_T",
"SPECIFICITY I", "SPECIFICITY II", "STAINING", "TARGET REMOVAL".
writeToFile
flag specifying whether the output should be saved as ReportPlot
numeric.names
if TRUE and writeToFile is TRUEsubstitute the plot options in the plot file name with digits
...
other arguments to createReportPlot
Value
plot as an object of type ReportPlot if writeToFile is TRUE and of class
ggplot otherwise.
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(RnBeads)
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: 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: GenomicRanges
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: MASS
Loading required package: RColorBrewer
Loading required package: cluster
Loading required package: ff
Loading required package: bit
Attaching package bit
package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit
Attaching package: 'bit'
The following object is masked from 'package:base':
xor
Attaching package ff
- getOption("fftempdir")=="/tmp/Rtmp15eLJI"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system
Attaching package: 'ff'
The following objects are masked from 'package:bit':
clone, clone.default, clone.list
The following objects are masked from 'package:utils':
write.csv, write.csv2
The following objects are masked from 'package:base':
is.factor, is.ordered
Loading required package: fields
Loading required package: spam
Loading required package: grid
Spam version 1.3-0 (2015-10-24) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
The following object is masked from 'package:stats4':
mle
The following objects are masked from 'package:base':
backsolve, forwardsolve
Loading required package: maps
# maps v3.1: updated 'world': all lakes moved to separate new #
# 'lakes' database. Type '?world' or 'news(package="maps")'. #
Attaching package: 'maps'
The following object is masked from 'package:cluster':
votes.repub
Loading required package: ggplot2
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Loading required package: gridExtra
Attaching package: 'gridExtra'
The following object is masked from 'package:BiocGenerics':
combine
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.
Loading required package: illuminaio
Loading required package: methylumi
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")'.
Attaching package: 'Biobase'
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: scales
Loading required package: reshape2
Loading required package: FDb.InfiniumMethylation.hg19
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:MASS':
select
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: org.Hs.eg.db
Loading required package: minfi
Loading required package: lattice
Loading required package: SummarizedExperiment
Attaching package: 'SummarizedExperiment'
The following object is masked from 'package:matrixStats':
rowRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following objects are masked from 'package:ff':
mismatch, pattern
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)
Loading required package: plyr
Attaching package: 'plyr'
The following object is masked from 'package:XVector':
compact
The following object is masked from 'package:matrixStats':
count
The following object is masked from 'package:maps':
ozone
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
Warning message:
replacing previous import 'gridExtra::combine' by 'methylumi::combine' when loading 'RnBeads'
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RnBeads/rnb.plot.control.boxplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: rnb.plot.control.boxplot
> ### Title: rnb.plot.control.boxplot
> ### Aliases: rnb.plot.control.boxplot
>
> ### ** Examples
>
> ## No test:
> library(RnBeads.hg19)
> data(small.example.object)
> rnb.plot.control.boxplot(rnb.set.example)
> ## End(No test)
>
>
>
>
>
>
> dev.off()
null device
1
>