convertCdf: Converts a CDF into the same CDF but with another format

Description

Converts a CDF into the same CDF but with another format. Currently only CDF files in version 4 (binary/XDA) can be written. However, any input format is recognized.

Usage

convertCdf(filename, outFilename, version="4", force=FALSE, ..., .validate=TRUE, verbose=FALSE)

Arguments

filename

The pathname of the original CDF file.

outFilename

The pathname of the destination CDF file. If the same as the source file, an exception is thrown.

version

The version of the output file format.

force

If FALSE, and the version of the orignal CDF is the same as the output version, the new CDF will not be generated, otherwise it will.

...

Not used.

.validate

If TRUE, a consistency test between the generated and the original CDF is performed. Note that the memory overhead for this can be quite large, because two complete CDF structures are kept in memory at the same time.

verbose

If TRUE, extra details are written while processing.

Value

Returns (invisibly) TRUE if a new CDF was generated, otherwise FALSE.

Benchmarking of ASCII and binary CDFs

Binary CDFs are much faster to read than ASCII CDFs. Here are some example for reading complete CDFs (the differnce is even larger when reading CDFs in subsets):

HG-U133A (22283 units): ASCII 11.7s (9.3x), binary 1.20s (1x).
Hu6800 (7129 units): ASCII 3.5s (6.1x), binary 0.57s (1x).

Confirmed convertions to binary (XDA) CDFs

The following chip types have been converted using convertCdf() and then verified for correctness using compareCdfs(): ASCII-to-binary: HG-U133A, Hu6800. Binary-to-binary: Test3.

Examples

Run this code

##############################################################
if (require("AffymetrixDataTestFiles")) {            # START #
##############################################################


chipType <- "Test3"
cdfFiles <- findCdf(chipType, firstOnly=FALSE)
cdfFiles <- list(
  ASCII=grep("ASCII", cdfFiles, value=TRUE),
  XDA=grep("XDA", cdfFiles, value=TRUE)
)

outFile <- file.path(tempdir(), sprintf("%s.cdf", chipType))
convertCdf(cdfFiles$ASCII, outFile, verbose=TRUE)

##############################################################
}                                                     # STOP #
##############################################################

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