read.metharray.exp {minfi} | R Documentation

## Reads an entire metharray experiment using a sample sheet

### Description

Reads an entire methylation array experiment using a sample sheet or (optionally) a target like data.frame.

### Usage

    read.metharray.exp(base = NULL, targets = NULL, extended = FALSE,
        recursive = FALSE, verbose = FALSE, force = FALSE)

### Arguments

`base` | The base directory.
`targets` | A targets `data.frame`, see details
`extended` | Should the output of the function be a `"RGChannelSetExtended"` (default is `"RGChannelSet"`).
`recursive` | Should the search be recursive (see details)
`verbose` | Should the function be verbose?
`force` | Should reading different size IDAT files be forced? See the documentation for `read.metharray`

### Details

If the `targets` argument is `NULL`, the function finds all two-color IDAT files in the directory given by `base`. If `recursive` is `TRUE`, the function searches `base` and all subdirectories. A two-color IDAT files are pair of files with names ending in `_Red.idat` or `_Grn.idat`.

If the `targets` argument is not `NULL` it is assumed it has a columned named `Basename`, and this is assumed to be pointing to the base name of a two color IDAT file, ie. a name that can be made into a real IDAT file by appending either `_Red.idat` or `_Grn.idat`.

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

### Value

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

### Author(s)

Kasper Daniel Hansen khansen@jhsph.edu.

### See Also

`read.metharray` for the workhorse function, `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.exp(file.path(baseDir, "5723646052"))

    }

[Package minfi version 1.34.0 Index]