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Department of Bioinformatics and Computational Biology

GeneClust S-Plus User’s Guide

Gene Shaving is a method for clustering groups of similarly behaving genes whose changes in expression are most tightly linked to observed biological changes. The basic method is similar to observed principal components (singular value decomposition, maximum eigenvalue, etc.) with a sequential twist: a canonical “gene vector” is identified based on the eigenvectors, and the genes are ranked according to their agreement with this vector. The worst fitting are then “shaved off” and a new canonical vector is identified and fit.

The GeneClust distribution consists of a Java front-end for an S-plus back-end which calls various C functions implementing the statistical method. A pseudoterminal application qua agent accepts commands from the Java front-end and returns output from S-plus.

User Interface

The Java application can process raw data or generate its own. The information input by the user is checked for validity. Invalid input will cause the offending field to be displayed in reverse video. ToolTips with numeric range information are provided.

GeneClust in Raw Data Mode

GeneClust in Demo Mode

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File Pulldown Menu

The File pulldown menu contains all the generic file handling options.

  • Open…: Reads settings from a configuration file.
  • Save…: Write current settings to a configuration file.
  • Quit: Quits the application.

Help Pulldown Menu

The Help pulldown menu contains all the options providing basic assistance in using the application.

  • Overview: Provides a high level description of the application’s purpose.
  • User Guide: Displays this document via web browser.
  • About: Provides information about the application itself.

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Input/Output

  • Environment variables:
    • GCHOME: Root directory of the installation. Mandatory.
    • GCDATA: Default directory for data files. Defaults to $GCHOME/data directory if unset.
    • GCOUTPUT: Directory for saving simulation output files. Defaults to $GCHOME/output directory if unset.
  • Files:
    • <settings>.cf: Configuration file used to store simulation settings.
    • <supervision>.clf: Classification file used to perform supervised shaving.
    • <datafile>.tsv: ASCII file that contains tab-separated values.
  • Command line activation:
    java
    • Dgeneclust.home=pathname Specifies same thing as $GCHOME
    • Dgeneclust.data=pathname Specifies same thing as $GCDATA
    • Dgeneclust.output=pathname Specifies same thing as $GCOUTPUT
    • Dsplus.home=pathname Specifies same thing as $SHOME
    • Dsplus.exec=splus_filename Specifies the name of the S-plus executable
    • Djava.security.policy=java/policy/GeneClust.policy Specifies the Java security policy file
    • jar java/jars/GeneClust.jar Specifies the GUI application archive
      [config_filename] Specifies an existing GeneClust configuration file to open on startup

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