minfi (version 1.18.2)

read.metharray: Parsing IDAT files from Illumina methylation arrays.

Description

Parsing IDAT files from Illumina methylation arrays.

Usage

read.metharray(basenames, extended = FALSE, verbose = FALSE)

Arguments

basenames

The basenames or filenames of the IDAT files. By basenames we mean the filename without the ending _Grn.idat or _Red.idat (such that each sample occur once). By filenames we mean filenames including _Grn.idat or _Red.idat (but only one of the colors)

extended

Should a RGChannelSet or a RGChannelSetExtended be returned.

verbose

Should the function be verbose?

Value

• An object of class RGChannelSet or RGChannelSetExtended.

Details

The type of methylation array is guess by looking at the number of probes in the IDAT files.

See Also

read.metharray.exp for a convenience function for reading an experiment, read.metharray.sheet for reading a sample sheet and RGChannelSet for the output class.

Examples

if(require(minfiData)) {

baseDir <- system.file("extdata", package = "minfiData")
RGSet <- read.metharray(file.path(baseDir, "5723646052",
    c("5723646052_R02C02", "5723646052_R04C01")))

}