findCdf {affxparser} | R Documentation |
Search for CDF files in multiple directories.
findCdf(chipType=NULL, paths=NULL, recursive=TRUE, pattern="[.](c|C)(d|D)(f|F)$", ...)
chipType |
A character string of the chip type to search for. |
paths |
A character vector of paths to be searched.
The current directory is always searched at the beginning.
If NULL , default paths are searched. For more details, see below. |
recursive |
If TRUE , directories are searched recursively. |
pattern |
A regular expression file name pattern to match. |
... |
Additional arguments passed to findFiles (). |
Note, the current directory is always searched first, but never recursively (unless it is added to the search path explicitly). This provides an easy way to override other files in the search path.
If paths
is NULL
, then a set of default paths are searched.
The default search path consitutes:
getOption("AFFX_CDF_PATH")
Sys.getenv("AFFX_CDF_PATH")
One of the easiest ways to set system variables for R is to
set them in an .Renviron
file, e.g.
# affxparser: Set default CDF path AFFX_CDF_PATH=${AFFX_CDF_PATH};M:/Affymetrix_2004-100k_trios/cdf AFFX_CDF_PATH=${AFFX_CDF_PATH};M:/Affymetrix_2005-500k_data/cdfSee
Startup
for more details.
Returns a vector
of the full pathnames of the files found.
Henrik Bengtsson (http://www.braju.com/R/)
This method is used internally by readCelUnits
() if the CDF
file is not specified.
############################################################## 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 # ##############################################################