gtypeCelToPQ: Function to immitate Affymetrix' gtype_cel_to_pq software

In HenrikBengtsson/aroma.apd: A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]

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 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.

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)
}

HenrikBengtsson/aroma.apd documentation built on Jan. 31, 2024, 8:17 a.m.