| gtypeCelToPQ {aroma.apd} | R Documentation |
Function to immitate Affymetrix' gtype_cel_to_pq software.
## Default S3 method: gtypeCelToPQ(filename, units=NULL, ..., cdf=NULL, nbrOfQuartets=NULL, verbose=FALSE)
filename |
The name of a CEL file. |
units |
Indices of CDF units to be returned. |
... |
Arguments passed to readCelUnits. |
cdf |
A CDF list structure, the pathname of the CDF file, or
NULL. If NULL, the CDF file corresponding to the chip type of
the CEL file is searched for using findCdf. |
nbrOfQuartets |
The number of probe quartets in the returned
matrix. |
verbose |
See Verbose. |
Returns an NxK matrix where N is the number of probesets (SNPs) and
K=4*Q where Q is the number of probe quartets (PMA,MMA,PMB,MMB).
The rownames corresponds to the probeset names.
Henrik Bengtsson (http://www.braju.com/R/)
[1] Affymetrix, Understanding Genotyping Probe Set Structure, 2005.
http://www.affymetrix.com/support/developer/whitepapers/genotyping_probe_set_structure.affx
gtypeCelToPQ().
applyCdfGroups.
# Scan for CEL files
files <- list.files(pattern="[.](c|C)(e|E)(l|L)$")
# Convert each to RAW file
for (file in files) {
rawFile <- gsub("[.][^.]*$", ".raw", file)
file.remove(rawFile)
cel <- gtypeCelToPQ(file, verbose=TRUE)
write.table(file=rawFile, cel, sep="\t", quote=FALSE)
rm(file, rawFile, cel)
gc()
}
# Clean up
rm(files)