convertCel {affxparser} | R Documentation |
Converts a CEL into the same CEL but with another format. Currently only CEL files in version 4 (binary/XDA) can be written. However, any input format is recognized.
convertCel(filename, outFilename, readMap=NULL, writeMap=NULL, version="4", ..., .validate=FALSE, verbose=FALSE)
filename |
The pathname of the original CEL file. |
outFilename |
The pathname of the destination CEL file. If the same as the source file, an exception is thrown. |
readMap |
An optional read map for the input CEL file. |
writeMap |
An optional write map for the output CEL file. |
version |
The version of the output file format. |
... |
Not used. |
.validate |
If TRUE , a consistency test between the generated
and the original CEL is performed. |
verbose |
If TRUE , extra details are written while processing. |
Returns (invisibly) TRUE
if a new CEL was generated, otherwise FALSE
.
Binary CELs are much faster to read than ASCII CELs. Here are some example for reading complete CELs (the differnce is even larger when reading CELs in subsets):
Henrik Bengtsson (http://www.braju.com/R/)
createCel
().
############################################################## if (require("AffymetrixDataTestFiles")) { # START # ############################################################## # Search for some available Calvin CEL files path <- system.file("rawData", package="AffymetrixDataTestFiles") files <- findFiles(pattern="[.](cel|CEL)$", path=path, recursive=TRUE, firstOnly=FALSE) files <- grep("FusionSDK_Test3", files, value=TRUE) files <- grep("Calvin", files, value=TRUE) file <- files[1] outFile <- file.path(tempdir(), gsub("[.]CEL$", ",XBA.CEL", basename(file))) if (file.exists(outFile)) file.remove(outFile) convertCel(file, outFile, .validate=TRUE) ############################################################## } # STOP # ##############################################################