Add probe color channel and basic annotation information based on the annotation library of Illumina methylation microarray

Description

Add probe color channel and basic annotation information based on the annotation library of Illumina methylation microarray

Usage

addAnnotationInfo(methyLumiM, lib = 'FDb.InfiniumMethylation.hg19', annotationColumn=c('COLOR_CHANNEL', 'CHROMOSOME', 'POSITION'))

Arguments

Details

The "lib" parameter supports both FeatureDb based annotation libraries and old array-based annotation libraries. 'FDb.InfiniumMethylation.hg19' is the FeatureDb based annotation library, which includes both 450k and 27k data. "IlluminaHumanMethylation27k.db" (for 27k array) and "IlluminaHumanMethylation450k.db" (450k infinium array) are old types of annotation libraries.

Value

return the MethyLumiM object with COLOR_CHANNEL, CHROMOSOME and chromome POSITION information added to the featureData.

Author(s)

Pan DU

See Also

lumiMethyR

Examples

	data(example.lumiMethy)
	head(pData(featureData(example.lumiMethy)))
	## removing color channel information
	# testData = example.lumiMethy
	# pData(featureData(testData))$COLOR_CHANNEL = NULL
	# testData = addAnnotationInfo(testData, lib="IlluminaHumanMethylation27k.db")
	## check whether the color channel information is added
	# head(pData(featureData(testData)))
	

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.
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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/addAnnotationInfo.Rd_%03d_medium.png", width=480, height=480)
> ### Name: addAnnotationInfo
> ### Title: Add probe color channel and basic annotation information based
> ###   on the annotation library of Illumina methylation microarray
> ### Aliases: addAnnotationInfo
> ### Keywords: methods
> 
> ### ** Examples
> 
> 	data(example.lumiMethy)
> 	head(pData(featureData(example.lumiMethy)))
           CHR COLOR_CHANNEL
cg00002426   3           Red
cg00012386   1           Red
cg00013618  22           Grn
cg00014837  12           Red
cg00020533   6           Red
cg00021527  17           Red
> 	## removing color channel information
> 	# testData = example.lumiMethy
> 	# pData(featureData(testData))$COLOR_CHANNEL = NULL
> 	# testData = addAnnotationInfo(testData, lib="IlluminaHumanMethylation27k.db")
> 	## check whether the color channel information is added
> 	# head(pData(featureData(testData)))
> 	
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>