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PILISModelTrainer

Train the PILIS model with a given set of spectra and identifications

Experimental classes:
This TOPP-tool is not well tested and not all features might be properly implemented and tested!
pot. predecessor tools $ \longrightarrow $ PILISModelTrainer $ \longrightarrow $ pot. successor tools
MascotAdapter (or other ID engines) PILISIdentification
PILISModelCV PILISSpectraGenerator

In order to train the model, the parameters of the fragmentation model need to be set first. Via the -write_ini command line switch an ini file can be created, edited to the needs and used afterwards. Additionally, the spectra should be given as MSP file, which already contains identifications or as mzML files. When using mzML files, idXML files must be used to get the peptide sequence information for the spectra. The tool trains then a model using the spectra and the peptides and writes it to the file given in the parameter 'trained_model_file'. Additionally, a model can be given as starting point via the parameter 'model_file'. With the min_charge and max_charge parameters, the peptides can be restricted to the specified charge range.

The command line parameters of this tool are:

INI file documentation of this tool:


OpenMS / TOPP release 1.11.1 Documentation generated on Sun Sep 7 2014 06:42:38 using doxygen 1.8.8