Tool to estimate the false discovery rate on peptide and protein level
pot. predecessor tools | ![]() ![]() | pot. successor tools |
MascotAdapter (or other ID engines) | IDFilter | |
PeptideIndexer |
This TOPP tool can calculate the false discovery rate (FDR) given a forward and backward search (or one run on a combined database). Most useful is this on protein level, however, it also can be applied to peptides.
The false discovery rate is defined as the number of false discoveries (the hits in the reversed search) over the number of false and correct discoveries (the hits in both databases) with a score better than a given threshold.
Prerequisites:
When no decoy hits were found you will get a warning saying something like:
"FalseDiscoveryRate: #decoy sequences is zero! Setting all target sequences to q-value/FDR 0!"
This should be a serious concern, since the target/decoy annotation in a previous step has probably a misconfigured database (see PeptideIndexer).
The command line parameters of this tool are:
FalseDiscoveryRate -- Estimates the false discovery rate on peptide and protein level using decoy searches. Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976 Usage: FalseDiscoveryRate <options> This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti on or use the --helphelp option. Options (mandatory options marked with '*'): -in <file> Identification input file which contains a search against a concatenated sequence databa se. Either specify '-in' alone or 'fwd_in' together with 'rev_in' as input. (valid forma ts: 'idXML') -fwd_in <file> Identification input to estimate FDR, forward run. (valid formats: 'idXML') -rev_in <file> Identification input to estimate FDR, decoy run. (valid formats: 'idXML') -out <file>* Identification output with annotated FDR (valid formats: 'idXML') -proteins_only If set, the FDR of the proteins only is calculated -peptides_only If set, the FDR of the peptides only is calculated Common TOPP 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: - algorithm Parameter section for the FDR calculation algorithm 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:
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |