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

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DEPRECATED. Do not start building new projects based on this package. (The (in-house) APD file format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensities. Chip types can be added to APD file and similar to methods in the affxparser package, this package provides methods to read APDs organized by units (probesets). In addition, the probe elements can be arranged optimally such that the elements are guaranteed to be read in order when, for instance, data is read unit by unit. This speeds up the read substantially. This package is supporting the Aroma framework and should not be used elsewhere.)

Author
Henrik Bengtsson [aut, cre, cph]
Date of publication
2015-02-25 00:49:33
Maintainer
Henrik Bengtsson <henrikb@braju.com>
License
LGPL (>= 2.1)
Version
0.6.0
URLs

View on CRAN

Man pages

aroma.apd-package
Package aroma.apd
cdfToApdMap
Generates an APD read map file from an Affymetrix CDF file
celToApd
Generates an APD file from an Affymetrix CEL file
createApd
Creates an Affymetrix probe data (APD) file
findApdMap
Search for APD map files in multiple directories
gtypeCelToPQ
Function to immitate Affymetrix' gtype\_cel\_to\_pq software
Non-documented_objects
Non-documented objects
readApd
Reads an Affymetrix probe data (APD) file
readApdHeader
Reads the header of an Affymetrix probe data (APD) file
readApdMap
Reads an APD probe map file
readApdRectangle
Reads a spatial subset of probe-level data from Affymetrix...
readApdUnits
Reads Affymetrix probe data (APD) as units (probesets)
updateApd
Updates an Affymetrix probe data (APD) file
updateApdHeader
Updates the header of an Affymetrix probe data (APD) file
updateApdUnits
Updates an Affymetrix probe data (APD) file by units...
writeApd
Writes an APD probe data file
writeApdMap
Writes an APD probe map file

Files in this package

aroma.apd
aroma.apd/tests
aroma.apd/tests/readApdRectangle.R
aroma.apd/tests/gtypeCelToPQ.R
aroma.apd/tests/createApd.R
aroma.apd/tests/celToApd.R
aroma.apd/tests/writeApdMap.R
aroma.apd/tests/readApdUnits.R
aroma.apd/NAMESPACE
aroma.apd/NEWS
aroma.apd/R
aroma.apd/R/000.R
aroma.apd/R/readApdRectangle.R
aroma.apd/R/readApd.R
aroma.apd/R/gtypeCelToPQ.R
aroma.apd/R/cdfToApdMap.R
aroma.apd/R/createApd.R
aroma.apd/R/008.BioC.R
aroma.apd/R/findApdMap.R
aroma.apd/R/writeApd.R
aroma.apd/R/updateApd.R
aroma.apd/R/updateApdUnits.R
aroma.apd/R/celToApd.R
aroma.apd/R/writeApdMap.R
aroma.apd/R/updateApdHeader.R
aroma.apd/R/999.NonDocumentedObjects.R
aroma.apd/R/999.package.R
aroma.apd/R/zzz.R
aroma.apd/R/readApdUnits.R
aroma.apd/R/readApdHeader.R
aroma.apd/R/readApdMap.R
aroma.apd/MD5
aroma.apd/DESCRIPTION
aroma.apd/man
aroma.apd/man/writeApd.Rd
aroma.apd/man/updateApdUnits.Rd
aroma.apd/man/readApdHeader.Rd
aroma.apd/man/celToApd.Rd
aroma.apd/man/cdfToApdMap.Rd
aroma.apd/man/aroma.apd-package.Rd
aroma.apd/man/readApdRectangle.Rd
aroma.apd/man/writeApdMap.Rd
aroma.apd/man/readApdMap.Rd
aroma.apd/man/findApdMap.Rd
aroma.apd/man/updateApdHeader.Rd
aroma.apd/man/createApd.Rd
aroma.apd/man/updateApd.Rd
aroma.apd/man/gtypeCelToPQ.Rd
aroma.apd/man/readApdUnits.Rd
aroma.apd/man/readApd.Rd
aroma.apd/man/Non-documented_objects.Rd