addAnnotationInfo {lumi} | R Documentation |
Add probe color channel and basic annotation information based on the annotation library of Illumina methylation microarray
addAnnotationInfo(methyLumiM, lib = 'FDb.InfiniumMethylation.hg19', annotationColumn=c('COLOR_CHANNEL', 'CHROMOSOME', 'POSITION'))
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 |
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.
return the MethyLumiM object with COLOR_CHANNEL, CHROMOSOME and chromome POSITION information added to the featureData.
Pan DU
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)))