findCdf {affxparser} | R Documentation |
Search for CDF files in multiple directories.
findCdf(chipType=NULL, paths=NULL, pattern="[.](c|C)(d|D)(f|F)$", ...)
chipType |
A character string of the chip type to search for. |
paths |
A character vector of paths to be searched.
The current directory is always searched at the beginning.
If NULL , default paths are searched. For more details, see below. |
pattern |
A regular expression file name pattern to match. |
... |
Additional arguments passed to findFiles (). |
Note, the current directory is always searched at the beginning.
This provides an easy way to override other files in the search path.
If paths
is NULL
, then a set of default paths are searched.
The default search path is consituted of:
"."
"cdf/;data/cdf/"
getOption("AFFX_CDF_PATH")
Sys.getenv("AFFX_CDF_PATH")
One of the easiest ways to set system variables for R is to
set them in an .Renviron
file, e.g.
# affxparser: Set default CDF path AFFX_CDF_PATH=${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.
# Find a specific CDF file cdfFile <- findCdf("Mapping50K_Xba240") 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) }