Changeset 437:f225715c54d2 in orange-bioinformatics


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Timestamp:
07/31/08 12:35:10 (6 years ago)
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ales_erjavec <ales.erjavec@…>
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default
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  • doc/modules/obiKEGG.htm

    r421 r437  
    99<body> 
    1010<h1>obiKEGG: Interface to KEGG(Kyoto Encyclopedia of Genes and Genomes)</h1> 
    11 <p>obiKEGG is an interface to <a href="http://www.genome.jp/kegg/">Kyoto Encyclopedia of Genes and Genomes</a> that allows easy access to KEGG pathway and genes data.</p> 
     11<p>obiKEGG is an interface to <a href="http://www.genome.jp/kegg/">Kyoto Encyclopedia of Genes and Genomes</a> that allows easy access to KEGG pathway and gene data.</p> 
    1212 
    1313<h2>Local data manipulation</h2> 
     
    3030 
    3131<h2><index>KEGGOrganism</index></h2> 
     32<p><code>KEGGOrgansim</code> is a class for easy access to organism specific data.</p> 
     33<p class=section>Attributes</p> 
     34<dl class=attributes> 
     35    <dt>org</dt> 
     36    <dd>Kegg organism code (e.g. "hsa")</dd> 
     37    <dt>local_database_path</dt> 
     38    <dd>Path to the local database. If <code>None</code> the <code>obiKEGG.default_database_path</code> will be used</dd> 
     39</dl> 
     40<p class="header">Example: construction</p> 
     41<xmp class="code">org = KEGGOrganism("hsa", local_database_path="C:\\kegg")</xmp> 
    3242<p class=section>Methods</p> 
    3343<dl class=attributes> 
     
    7989</dl> 
    8090 
     91<h3>Example<h3> 
     92<p class="header">Getting enriched pathways</p> 
     93<xmp class="code">org = KEGGOrganism("hsa") 
     94genes, _, _ = org.get_unique_gene_ids([...]) 
     95res = orng.get_enriched_pathways(genes) 
     96for p_id, (genes, p_value, refCount) in res.items(): 
     97    print "Pathway id %s with p-value %.4f" %(p_id, p_value)</xmp> 
     98 
     99 
    81100<h2><index>KEGGPathway</index></h2> 
     101<p><code>KEGGPathway</code> is a class for pathway specific data</p> 
     102<p class=section>Attributes</p> 
     103<dl class=attributes> 
     104    <dt>pathway_id</dt> 
     105    <dd>Kegg pathway id code (e.g. "hsa:00052")</dd> 
     106    <dt>local_database_path</dt> 
     107    <dd>Path to the local database. If <code>None</code> the <code>obiKEGG.default_database_path</code> will be used</dd> 
     108</dl> 
    82109<p class=section>Methods</p> 
    83110<dl class=attributes> 
     
    104131     
    105132</dl> 
     133 
     134<h3>Example<h3> 
     135<p class="header">Retrieval of enriched pathway images with marked genes</p> 
     136<xmp class="code">for p_id, (genes, _, _) in res.items(): 
     137    pathway = KEGGPathway(p_id) 
     138    image = pathway.get_colored_image(genes) 
     139    image.save(p_id)</xmp> 
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