methylumIDAT {methylumi} | R Documentation

## methylumIDAT

### Description

Read a directory of methylumi idat files and return a `MethylumiSet`.

### Usage

    methylumIDAT(barcodes = NULL, pdat = NULL, parallel = F, n = F, n.sd =
    F, oob = T, idatPath=getwd(), ...)

### Arguments

`barcodes` | A vector of barcodes to read. Either this argument or `pdat` must be specified.
`pdat` | A data.frame describing the samples. A special column named "barcodes" can be used to specify the barcodes to be read.
`parallel` | If TRUE, an attempt will be made to process using multiple cores on a multicore machine.
`n` | Keep the bead numbers? (Default: no)
`n.sd` | Keep the bead-level SD? (Default: no)
`oob` | Keep the out-of-band (OOB) or opposite-channel signals? (Default: yes)
`idatPath` | The path to the directory containing the idat files.
`...` | Additional arguments to be passed to sub-functions.

### Details

Read a set of .idat files and return a `MethylumiSet` object. If you use this function to any significant degree in your analysis, we would appreciate your citing the paper describing it, "Low-level processing of Illumina Infinium DNA methylation beadarrays", TJ Triche, DJ Weisenberger, D Van Den Berg, KD Siegmund, and PW Laird, Nucleic acids research, 2013.

### Value

A `MethylumiSet` object.

### Author(s)

Tim Triche, Jr.

### See Also

The “methylumi450k“ vignette: vignette("methylumi450k", package="methylumi")

### Examples

    ## Not run:
    if(require('IlluminaHumanMethylation450k.db')) {
      barcodes <- c('6005486014_R04C02',
                  '6005486023_R05C01')
      lumi450k <- methylumIDAT(barcodes,idatPath=system.file('extdata/idat',package='methylumi')) # no normalization done
      sampleNames(lumi450k) <- c('TCGA1','TCGA2')
      show(lumi450k)
    }

    ## End(Not run)

[Package methylumi version 2.34.0 Index]