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, force = 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?

force

Should reading different size IDAT files be forced? See Details.

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.

We have seen IDAT files from the same array, but with different number of probes in the wild. Specifically this is the case for early access EPIC arrays which have fewer probes than final release EPIC arrays. It is possible to combine IDAT files from the same inferred array, but with different number of probes, into the same RGChannelSet by setting force=TRUE. The output object will have the same number of probes as the smallest array being parsed; effectively removing probes which could have been analyzed.

Examples

Run this code

if(require(minfiData)) {

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

}