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)