findCdf: Search for CDF files in multiple directories

In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK

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

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