methylumIDAT {methylumi} | R Documentation |
Read a directory of methylumi idat files and return a MethylumiSet
.
methylumIDAT(barcodes = NULL, pdat = NULL, parallel = F, n = F, n.sd = F, oob = T, idatPath=getwd(), ...)
barcodes |
A vector of barcodes to read. Either this argument or |
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. |
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.
A MethylumiSet
object.
Tim Triche, Jr.
The “methylumi450k“ vignette: vignette("methylumi450k", package="methylumi")
## 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)