convertCdf {affxparser} | R Documentation

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

[Package affxparser version 1.56.0 Index]