Util to estimate probability of peptide hits
pot. predecessor tools | ![]() ![]() | pot. successor tools |
MascotAdapter (or other ID engines) | - | |
PeptideIndexer |
So far an estimation of the false score distribution with a gamma distribution and the correct score distribution with a gaussian distribution is performed. The probabilities are calculated using bayes law, similar to PeptideProphet. This implementation is much simpler than that of PeptideProphet.
IDDecoyProbability -- Estimates peptide probabilities using a decoy search strategy. WARNING: This util is deprecated. Version: 2.0.0 Mar 30 2016, 12:52:33, Revision: GIT-NOTFOUND Usage: IDDecoyProbability <options> This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript ion or use the --helphelp option. Options (mandatory options marked with '*'): -in <file> Identification input of combined forward decoy search (reindex with PeptideIndexer first ) (valid formats: 'idXML') -fwd_in <file> Identification input of forward run (valid formats: 'idXML') -rev_in <file> Identification input of decoy run (valid formats: 'idXML') -out <file>* Identification output with forward scores converted to probabilities (valid formats: 'idXML') Common UTIL options: -ini <file> Use the given TOPP INI file -threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1') -write_ini <file> Writes the default configuration file --help Shows options --helphelp Shows all options (including advanced) The following configuration subsections are valid: - decoy_algorithm Algorithm parameter subsection You can write an example INI file using the '-write_ini' option. Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor. Have a look at the OpenMS documentation for more information.INI file documentation of this tool:
For the parameters of the algorithm section see the algorithms documentation:
decoy_algorithm
OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 16:18:43 using doxygen 1.8.5 |