affxparserInfo {affxparser} | R Documentation

## Overview of the Affxparser package.

### Description

The package implements an interface to the Fusion SDK from Affymetrix.com.

### Usage

      affxparserInfo(fusion.license = FALSE, file.changes = FALSE)

### Arguments

`fusion.license` | display the license of the Fusion SDK (this will happen in a browser).
`file.changes` | display the changes made to the Fusion SDK.

### Details

This package implements an interface to the Fusion SDK from Affymetrix.com. This SDK (software development kit) is an open source library used for parsing the various files formats used by the Affymetrix platform.

The intention is to provide interfaces to most if not all file formats which may be parsed using Fusion.

The SDK supports parsing of all the different versions of a specific fileformat. This means that ascii, binary as well as the new binary format (codename Calvin) used by Affymetrix is supported through a single API. We also expect any future changes to the file formats to be reflected in the SDK, and subsequently in this package.

However, as the current Fusion SDK does not support compressed files, neither does affxparser. This is in contrast to some of the existing code in affy and relatives (see below for links).

In general we aim to provide functions returning all information in the respective files. Currently it seems that future Affymetrix chip designs may consists of so many features that returning all information will lead to an unnecessary overhead on the case a user only wants access to a subset. We have tried to make this possible.

For older file, certain entries in the files have been removed from newer specifications, and the SDK does not provide utilities for reading these entries. This includes eg. the FEAT column of CDF files.

Currently the package as well as the Fusion SDK is in beta stage. Bugs may be related to either codebase. We are very interested in users being unable to compile/parse files using this library - this includes users with custom chip designs.

In addition, since we aim to return all information stored in the file (and accessible using the Fusion SDK) we would like reports from users being unable to do that.

The efficiency of the underlying code may vary with the version of the file being parsed. For example, we currently report the number of outliers present in a CEL file. In order to obtain this information from text based CEL files (version 2), the entire file needs to be read into memory. With version 3 of the file format, this information is stored in the header.

With the introduction of the Fusion SDK (and the next version of their file formats) Affymetrix has made it possible to use multibyte character sets. This implies that character information may be inaccesible if the compiler used to compile the c++ code does not support multibyte character sets (specifically we require that the R installation has defined the macro `SUPPORT_MCBS` in the `Rconfig.h` header file).

The `affxparserInfo` function returns relevant information regarding the version of the Fusion SDK (and possibly more). It simply echoes the README file in the package directory.

### Author(s)

James bullard, bullard@stat.berkeley.edu and Kasper Daniel Hansen, khansen@stat.berkeley.edu

### References

http://www.affymetrix.com, particular the support and developer parts of the website.

### See Also

Existing functions for parsing Affymetrix files may be found in affy, oligo, makecdfenv and makePlatformDesign.

### Examples

      affxparserInfo()

[Package affxparser version 1.2.0 Index]