importMethyIDAT: 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

Value

A MethyLumiM object

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.

Examples

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