aroma.apd-package {aroma.apd}

Package aroma.apd

Description

This package has been deprecated. Do not start building new projects based on it.

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.)

Requirements

This package requires the packages R.huge and affxparser.

Installation and updates

To install this package, see https://www.braju.com/R/.

To get started

To get started, see:

1. readApd(), readApdUnits(), readApdRectangle() - Reads APD files.

2. celToApd() - creates an APD file from a CEL file.

3. cdfToApdMap() - creates an APD read map from a CDF file.

4. findApdMap() - finds an APD read map.

5. createApd(), writeApd() - creates APD files.

6. updateApd(), updateApdUnits() - updates APD files.

Search paths

Typically you do not have to specify the pathname of the CDF file when reading APD files or similar. Instead, the chip type is obtained from the APD header and the corresponding APD file is search for in several predefined locations. For details how to specify the search path, see findCdf.

Some APD files uses a corresponding read map in order to read data faster. The findApdMap() method is used to find the corresponding APD map file containing the map vector. How to specify search paths for map files, see that method.

How to cite this package

Currently no information.

License

The releases of this package is licensed under LGPL version 2.1 or newer.

The development code of the packages is under a private licence (where applicable) and patches sent to the author fall under the latter license, but will be, if incorporated, released under the "release" license above.

References

[1] H. Bengtsson, The R.oo package - Object-Oriented Programming with References Using Standard R Code, In Kurt Hornik, Friedrich Leisch and Achim Zeileis, editors, Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003), March 20-22, Vienna, Austria. https://www.r-project.org/conferences/DSC-2003/Proceedings/

Author(s)

Henrik Bengtsson