findCdf {affxparser} | R Documentation

## Search for CDF files in multiple directories

### Description

Search for CDF files in multiple directories.

### Usage

    findCdf(chipType=NULL, paths=NULL, recursive=TRUE, pattern="[.](c|C)(d|D)(f|F)$", ...)

### Arguments

`chipType` | A `character` string of the chip type to search for.
`paths` | A `character` `vector` of paths to be searched. The current directory is always searched at the beginning. If `NULL`, default paths are searched. For more details, see below.
`recursive` | If `TRUE`, directories are searched recursively.
`pattern` | A regular expression file name pattern to match.
`...` | Additional arguments passed to `findFiles`().

### Details

Note, the current directory is always searched first, but never recursively (unless it is added to the search path explicitly). This provides an easy way to override other files in the search path.

If `paths` is `NULL`, then a set of default paths are searched. The default search path constitutes:

1. `getOption("AFFX_CDF_PATH")`

2. `Sys.getenv("AFFX_CDF_PATH")`

One of the easiest ways to set system variables for R is to set them in an `.Renviron` file, e.g.

        # affxparser: Set default CDF path
        AFFX_CDF_PATH=${AFFX_CDF_PATH};M:/Affymetrix_2004-100k_trios/cdf
        AFFX_CDF_PATH=${AFFX_CDF_PATH};M:/Affymetrix_2005-500k_data/cdf

See `Startup` for more details.

### Value

Returns a `vector` of the full pathnames of the files found.

### Author(s)

Henrik Bengtsson

### See Also

This method is used internally by `readCelUnits`() if the CDF file is not specified.

### Examples

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

    # Find a specific CDF file
    cdfFile <- findCdf("Mapping10K_Xba131")
    print(cdfFile)

    # Find the first CDF file (no matter what it is)
    cdfFile <- findCdf()
    print(cdfFile)

    # Find all CDF files in search path and display their headers
    cdfFiles <- findCdf(firstOnly=FALSE)
    for (cdfFile in cdfFiles) {
      cat("=======================================\n")
      hdr <- readCdfHeader(cdfFile)
      str(hdr)
    }

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

[Package affxparser version 1.56.0 Index]