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

In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK

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 original 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 difference 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 conversions 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.

Author(s)

Henrik Bengtsson

See Also

See compareCdfs() to compare two CDF files. writeCdf().

Examples

##############################################################
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 #
##############################################################

HenrikBengtsson/affxparser documentation built on Feb. 9, 2024, 3:13 a.m.