read.metharray {minfi} | R Documentation

## 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.

### 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.

### Value

An object of class `RGChannelSet` or `RGChannelSetExtended`.

### Author(s)

Kasper Daniel Hansenkhansen@jhsph.edu.

### 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")
    RGset1 <- read.metharray(file.path(baseDir, "5723646052", "5723646052_R02C02"))

    }

[Package minfi version 1.38.0 Index]