Read a directory of methylumi idat files and return a `MethyLumiSet`.
Usage
methylumIDAT(
barcodes = NULL,
pdat = NULL,
parallel = FALSE,
n = FALSE,
n.sd = FALSE,
oob = TRUE,
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.
Examples
if (FALSE) { # \dontrun{
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)
}
} # }