lumiMethyR {lumi} | R Documentation

## 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
`qcfile` | parameter of `methylumiR` function
`sampleDescriptions` | parameter of `methylumiR` function
`sep` | parameter of `methylumiR` function

### 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.

### Value

return a MethyLumiM object

### Author(s)

Pan Du

### See Also

See Also `importMethyIDAT`, `methylumiR` and `addControlData2methyLumiM`

[Package lumi version 2.40.0 Index]