Command-Line Version of the Ontologizer
This how-to describes the command-line version of the Ontologizer. This version can be used for batch processing or pipelines. Most general users will prefer the Java WebStart version, though. At first, download the .jar file.
Invoking
Ontologizer is a Java-Application and needs to be started via the 'java' command and be invoked with a plenty of arguments. All possible command arguments can be viewed via the --help argument. E.g. java -jar Ontologizer.jar --help. Here is a full list of options:| Short Option | Long Option | Explanation |
|---|---|---|
| -m | --mtc | Specifies the MTC method to use. Possible values are: "Bonferroni" (default), "None", "Westfall-Young-Single-Step" |
| -c | --calculation | Specifies the calculation method to use. Possible values are: "Parent-Child-Union", "Parent-Child-Intersection", "Term-For-Term" (default). For a full list, consult the output of the -h option. |
| -a | --association | File containing associations from genes to GO terms. Required |
| -d | --dot | For every studyset analysis write out an additional .dot file (GraphViz) containing the GOTerm graph with significant nodes. The optional argument in range between 0 and 0.5 specifies the maximum level on which a term is considered as significantly enriched. By appending a GO Term identifier (separated by a comma) the output is restriced to the subgraph originating at this GO Term. |
| -f | --filter | Filter the gene names by appling rules in a given file (currently only mapping supported). |
| -g | --go | Path to gene_ontology_edit.obo file (Required) |
| -h | --help | Shows this help |
| -i | --ignore | Ignore genes to which no association exist within the calculation. |
| -n | --annotation | Create an additional file per study set which contains the annotations. |
| -o | --outdir | Specfies the directory in which the results will be placed. |
| -p | --population | File containing genes within the population. Required |
| -r | --resamplingsteps | Specifies the number of steps used in resampling based MTCs |
| -s | --studyset | File of the study set or a directory containing study set files. Required |
| -v | --version | Shows version information and exits |
Instructions for Running the Ontologizer
In order to do something useful, Ontologizer must be started with several arguments (as indicated with "Required" within the output above).
First, you are required to specify the -g (or --go) option. This defines the path to a file which contains the GO terminology and structure. Ontologizer is able to parse files in the OBO format. Such are available directly at the GO Website.
Second, you are required to specify the -a option which defines the mapping of gene names to GO terms. The GO Website provides association files for a variety of organisms, as well.
Third, you must specify a population file with the -p option. This file contains all gene names (one per line) of the population set, e.g. the names of the genes of your microarray.
Last, you need to specify the path to your study set(s) with the -s option.. This can eighter be a single file for a single study set or a directory, in which case all files (ending with *.txt) are considered as separate study sets. As for the population file, one line represents only a single gene name.
When started with these four parameters only, the output of Ontologizer's calculation is written to a basic ascii table file into the same directory where the study files are located. The table's filename is derived from the name of the study set in question but prepended with "table-" string.
Using the -d option, you can instruct Ontologizer to create a graphical output of the results. For every study set, a file (name is prepended with "view-") is written which can be read by the graphviz 'dot' tool to produce a viewable graphics file. In this file, terms are depicted by nodes and their hierachical relations are depicted by edges. Because the GO DAG contains a huge amount of terms, the graph is constructed only for signifant terms and their predecessors (up to the source) and those significant terms are highligthed. Which terms are considered as significant is influenced by their p-values and the significance threshold. This threshold is specified as a parameter to the -d argument. It must be a valid floating point value ranging from 0 to 0.5. For example use "-d 0.05" to define those terms as significant whose p-value falls below 0.05.
In addition, you can specify a GO Term ID, after the floating-point value (separated by ","). In this case only the subgraph starting at this term is written. For example use "-d 0.05,8152" to get only a graph with the term id GO:0008152 (metabolism) and its successors within the subgraph emanating from GO:0008152 such that all significantly overrepresented terms are included in the graph.
Some sample datasets and population sets can be downloaded from this page.
java -jar Ontologizer.jar -a gene_association.sgd -g gene_ontology.obo -s study/4hourSMinduced.txt -p population.txt -c Parent-Child-Union -m Westfall-Young-Single-Step -d 0.05 -r 1000
dot -Tpng view-4hourSMinduced-Parent-Child-Westfall-Young-Single-Step.dot -oExample.png
