Module: SLiMGOER Description: Short Linear Motif GO Enrichment of RLC Version: 0.1 Last Edit: 16/09/08

Copyright © 2008 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_go rje_zen

See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This module looks for enriched RLC scores for a given SLiM over its reversed/scrambled versions for GO categories. Initial versions of this module are simply for proof of principle analysis, coverting SLiMSearch results into a table for R analysis. Later versions will hopefully incorporate the SLiMSearch and statistical tests too.

Commandline

INPUT/OUTPUT

resfile=FILE : Basefile for SLiMSearch results CSV files []
minocc=X : Minimum number of occurrences for a given Motif/GO combo [5]
minhom=X : Minimum number of homologues for each protein [3]
maxgenes=X : Maximum number of genes for a GO term to apply to [2000]

See also rje.py generic commandline options.

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.1 - Modifications to improve functionality, reduce run times and return better data.