aroma.apd (version 0.7.0)

gtypeCelToPQ: Function to immitate Affymetrix' gtype_cel_to_pq software

Description

Function to immitate Affymetrix' gtype_cel_to_pq software.

Usage

# S3 method for default
gtypeCelToPQ(filename, units=NULL, ..., cdf=NULL, nbrOfQuartets=NULL, verbose=FALSE)

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.

Arguments

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.

Author

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)
}