gtypeCelToPQ {aroma.apd} | R Documentation |
Function to immitate Affymetrix' gtype_cel_to_pq software
Description
Function to immitate Affymetrix' gtype_cel_to_pq software.
Usage
## Default S3 method:
gtypeCelToPQ(filename, units=NULL, ..., cdf=NULL, nbrOfQuartets=NULL, verbose=FALSE)
Arguments
filename |
The name of a CEL file. |
units |
Indices of CDF units to be returned. |
... |
Arguments passed to |
cdf |
A CDF |
nbrOfQuartets |
The number of probe quartets in the returned
|
verbose |
See |
Value
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.
Author(s)
Henrik Bengtsson
References
[1] Affymetrix, Genotyping Probe Set Structure, Developers' Network, White paper, 2005-2015.
See Also
gtypeCelToPQ
().
applyCdfGroups
.
Examples
# Scan for CEL files
files <- list.files(pattern="[.](cel|CEL)$")
# Convert each to RAW file
for (file in files) {
rawFile <- gsub("[.][^.]*$", ".raw", file)
file.remove(rawFile)
cel <- gtypeCelToPQ(file, verbose=TRUE)
write.table(file=rawFile, cel, sep="\t", quote=FALSE)
}
[Package aroma.apd version 0.7.0 Index]