lumiMethyR:
Reading Illumina methylation microarray data
Description
This function is a wrap of methylumiR function in methylumi package.
Usage
lumiMethyR(filename, lib=NULL, controlData=NULL, qcfile=NULL, sampleDescriptions=NULL, sep = NULL)
Arguments
filename
file name output by GenomeStudio
lib
Annotation library of Illumina methylation microarray
controlData
the controlData file name or a MethyLumiQC object to be added to the "controlData" slot of the MethyLumiM object
Details
This function is a wrap of methylumiR function in methylumi package. It will coerce the returned object as MethyLumiM class. The methylated and unmethylated probe intensity information is required for color-bias adjustment and normalization. If users have the Illumina IDAT files, we suggest use importMethyIDAT function to import the data. The importMethyIDAT function will automatically retrieve the required information and return a MethyLumiM object.