importMethyIDAT: Import Illumina methylation .idat files as an MethyLumiM...

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

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

lumi documentation built on Nov. 8, 2020, 5:27 p.m.