As TOPP offers no functionality for statistical analysis, this step is normally done using external statistics packages. @n In order to export the %OpenMS XML formats into an appropriate format for these packages the TOPP @b TextExporter can be used. It converts the the following %OpenMS XML formats to text files: - FeatureXML - IdXML - ConsensusXML The use of the @b TextExporter is very simple:
%OpenMS offers a lot of visualization and analysis functionality for feature data. @n Feature data in text format, e.g. from other analysis tools, can be imported using the @b TextImporter. The default mode accepts comma separated values containing the following columns: RT, m/z, intensity. Additionally meta data columns may follow. If meta data is used, meta data column names have to be specified in a header line. Without headers:
1201 503.123 1435000 1201 1006.246 1235200
Or with headers:
RT m/z Int isHeavy myMeta 1201 503.123 1435000 true 2 1201 1006.246 1235200 maybe 1
Example invocation:
The tool also supports data from msInspect,SpecArray and Kroenik(Hardkloer sibling), just specify the -mode option accordingly.
Peptide/protein identification data from several identification engines can be converted to idXML format using the @b IDFileConverter tool. It can currently read the following formats: - Sequest output folder - pepXML file - idXML file It can currently write the folling formats: - pepXML - idXML This example shows how to convert pepXML to idXML:
OpenMS / TOPP release 1.9.0 | Documentation generated on Tue May 28 2013 12:41:58 using doxygen 1.8.3.1 |