methylumIDAT: methylumIDAT

In seandavi/methylumi: Handle Illumina methylation data

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)

seandavi/methylumi documentation built on Oct. 28, 2021, 12:42 a.m.