addAnnotationInfo: 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

methyLumiM

a MethyLumiM object includes Illumina Infinium methylation data

lib

Annotation library of Illumina methylation microarray.

annotationColumn

only include 'COLOR_CHANNEL', 'CHROMOSOME' and 'POSITION' information

Value

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

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.

Examples

Run this code

	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)))