methylumi (version 2.12.0)

methylumIDAT: 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

n.sd

oob

idatPath

The path to the directory containing the idat files.

...

Value

A MethylumiSet object.

Details

Read a set of .idat files and return a MethylumiSet object.

See Also

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)