.idat files and initializes an object of type MethyLumiSet.
read.idat.files(base.dir, barcodes = NULL, sample.sheet = NULL, sep.samples = rnb.getOption("import.table.separator"), useff = FALSE, verbose = TRUE).idat files to be read; or a character vector of such
directories.character vector listing the barcodes of the samples that should be
loaded. If supplied, this vector must not contain NA among its elements.data.frame or matrix. Only (and all) samples defined in this
table will be loaded. The table is expected to contain a column named "barcode" that
lists the samples' Sentrix barcodes. If such a column is not present, this function searches
for columns "Sentrix_ID" and "Sentrix_Position" (or similar) that build a
barcode.character string used as field separator in the sample sheet file.
Default value is taken by the call to rnb.getOption("import.table.separator")TRUE ff package is used to store large matrices on the hard diskMethyLumiSet.
barcodes, nor sample.sheet are specified, the function attempts to locate a file in
base.dir containing sample annotation information. It fails ifsuch a file cannot be (unambiguously)
identified. If both barcodes and sample.sheet are supplied, only sample.sheet is used in loading
methylation data. The value of barcodes is tested for validity but it is not used as a filter.
methylumIDAT in package methylumi