Arguments
base.dir
Directory that contains the .idat files to be read; or a character vector of such
directories.
barcodes
Optional non-empty character vector listing the barcodes of the samples that should be
loaded. If supplied, this vector must not contain NA among its elements.
sample.sheet
Optional file name containing a table of sample annotation data, or the table itself in the
form of a 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. sep.samples
character used as field separator in the sample sheet file.
Default value is taken by the call to rnb.getOption("import.table.separator")
load.chunk
integer of size one, giving the number of IDAT files which should be loaded in
one loading cycle or NULL, in which case an attempt will be made to load all files
in one go. Should be assigned in case the number of IDATs is more than one thousand.
keep.methylumi
a flag indicating whether the a MethyLumiSet
object should be returned instead of a RnBeadRawSet.
verbose
Flag indicating ifthe messages to the logger should be sent. Note that the logger
must be initialized prior to calling this function. Logging is useful for keeping a
record of the downloaded and processed samples. Also, informative messages are
stored in case of an error.