importMethyIDAT {lumi} | R Documentation

## Import Illumina methylation .idat files as an MethyLumiM object

### Description

Import Illumina methylation .idat files as an MethyLumiM object. An extension of `lumIDAT` function

### Usage

    importMethyIDAT(sampleInfo, dataPath = getwd(), lib = NULL, bigMatrix=FALSE, dir.bigMatrix='.', savePrefix.bigMatrix, ...)

### Arguments

`sampleInfo` | A data.frame of sample information or a character vector of barcodes.
`dataPath` | The path of .idat files
`lib` | Annotation library
`bigMatrix` | whether to save the data as BigMatrix (designed for very large dataset)
`dir.bigMatrix` | the parent directory to save the BigMatrix data files
`savePrefix.bigMatrix` | the folder name prefix of the directory to save the BigMatrix data files. The fold name will be like this: paste(savePrefix.bigMatrix, '_bigmat', sep=”)
`...` | other parameters used by `lumIDAT` function

### Details

This function is an extension of `lumIDAT`. It adds sample information and probe annotation information to the data. As Illumina organizes the output .idat files by barcodes, the function will automatically check the sub-folders in the names of barcodes for .idat files. The "sampleInfo" parameter can be either a barcode vector, e.g., "7310440039_R04C02" "7310440039_R05C02". Or a data.frame with required columns of 'Sentrix_Barcode' and 'Sentrix_Position'. If "sampleInfo" is a data.frame, it will be added as the pData of the output MethyLumiM object.

### Value

A MethyLumiM object

### Author(s)

Pan Du, Tim Triche

### See Also

`lumIDAT`, `lumiMethyR`, `addAnnotationInfo`

[Package lumi version 2.40.0 Index]