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0.3.1 2011-03-29
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0.2.1 2011-01-19
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0.1.1 2011-01-15
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README 2011-03-28 1.7 kB
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Hoea: a python module for hierarchical ontology enrichment analysis

Hoea is a python module for hierarchical ontology enrichment analysis, which
facilitated GO (Gene Ontology)/KO (KEGG Orthology) enrichment analysis at any desktop.

Tutorails and documentations are available at:  http://hoea.sourceforge.net/.
Usage: Hoea.py -i <input file 1> -j [input file 2] -r ho.relation -d ho.definition -a annotation_file -s output_prefix -p pvalue_cutoff -n number_cutoff -e graph_level

Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  -i INPUT1, --input1=INPUT1
                        input file for analysis
  -j INPUT2, --input2=INPUT2
                        input another file for analysis [optional]
  -r HOREL, --ho-relation=HOREL
                        ho relation file
  -d HODEF, --ho-definition=HODEF
                        ho definition file
  -a ANNOTATION, --annotation=ANNOTATION
                        annotation file
  -p PVALUE, --pvalue=PVALUE
                        FDR adjust P-value cutoff of ho terms [default: 0.05]
  -n NUMBER, --number=NUMBER
                        number cutoff of an ho term with iterm assigned
                        [default: 5]
  -s PREFIX, --prefix=PREFIX
                        prefix of output file [default: file name of input
                        file 1]
  -e LEVEL, --level=LEVEL
                        graph level (1,2,3) [default: 3] [1 means full graph
                        with all nodes, 2 means any node of two connected
                        nodes was significant, 3 means both nodes were
                        significant]
Source: README, updated 2011-03-28