convertCel: Converts a CEL into the same CEL but with another format

Description Usage Arguments Value Benchmarking of ASCII and binary CELs WARNING: Changing the chip type label Author(s) See Also Examples

View source: R/convertCel.R

Description

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.

Usage

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convertCel(filename, outFilename, readMap=NULL, writeMap=NULL, version="4",
  newChipType=NULL, ..., .validate=FALSE, verbose=FALSE)

Arguments

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.

newChipType

(Only for advanced users who fully understands the Affymetrix CEL file format!) An optional string for overriding the chip type (label) in the CEL file header.

...

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.

Value

Returns (invisibly) TRUE if a new CEL was generated, otherwise FALSE.

Benchmarking of ASCII and binary CELs

Binary CELs are much faster to read than ASCII CELs. Here are some example for reading complete CELs (the difference is even larger when reading CELs in subsets):

WARNING: Changing the chip type label

The newChipType argument changes the label in the part of DAT header that specifies the chip type of the CEL file. Note that it does not change anything else in the CEL file. This type of relabeling is valid for updating the chip type label of CEL files that where generated during, say, an "Early Access" period leading to a different chip type label than what more recent CEL files of the same physical chip type have.

Author(s)

Henrik Bengtsson

See Also

createCel().

Examples

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

affxparser documentation built on Nov. 1, 2018, 2:25 a.m.