Generates an Affymetrix CDF file from a Platform Design (PD) package. Platform Design (PD) packages are also known as "pdInfo" packages.
## S3 method for class 'AffyGenePDInfo': writeCdf((this, tags=c("*"), unitsBy=c("transcript", "exon"), namesBy=c("fsetid", "id"), path=NULL, overwrite=FALSE, verbose=TRUE, ...))
- An optional
vectorof tags to be added to the CDF filename.
characterstring specifying how to group units.
- The output path where the CDF file is written. If
NULL(default), then it is written to the corresponding
TRUE, an existing CDF is overwritten, otherwise an exception is thrown.
- Not used.
The formal chip type of the CDF is inferred from the AffyGenePDInfo package. The filename of the CDF is constructed from the chip type and any optional tags. To minimize the risk for a corrupt CDF file, the creation of the file is atomic by first writing to a temporary file which is then renamed.
Returns (invisibly) the pathname to CDF written.
The information available in the PD package is limited and does not contain all information needed to populate a CDF file. In order to workaround these limitations, certain CDF entries are set to predefined/hardwired values. The 'pbase' and 'tbase' entries of the generated CDF file is hardwired to "T" and "A", respectively. Likewise, the 'groupdirection' entry is hardwired to "sense".
Documentation reproduced from package aroma.affymetrix, version 2.9.0. License: LGPL (>= 2.1)