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aroma.affymetrix (version 2.11.1)

writeCdf.AffyGenePDInfo: Generates an Affymetrix CDF file from a Platform Design (PD) package

Description

Generates an Affymetrix CDF file from a Platform Design (PD) package. Platform Design (PD) packages are also known as "pdInfo" packages.

Usage

## S3 method for class 'AffyGenePDInfo':
writeCdf(this, tags=c("*"), unitsBy=c("transcript", "exon"), namesBy=c("fsetid", "id"),
  path=NULL, overwrite=FALSE, verbose=TRUE, ...)

Arguments

tags
An optional character vector of tags to be added to the CDF filename.
unitsBy
A character string specifying how to group units.
path
The output path where the CDF file is written. If NULL (default), then it is written to the corresponding annotationData/chipTypes// directory.
overwrite
If TRUE, an existing CDF is overwritten, otherwise an exception is thrown.
verbose
A logical or Verbose.
...
Not used.

Value

  • Returns (invisibly) the pathname to CDF written.

Limitations

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".

Details

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.