OpenMS
2.4.0
|
Tool to estimate the false discovery rate on peptide and protein level
pot. predecessor tools | FalseDiscoveryRate | pot. successor tools |
MascotAdapter (or other ID engines) | IDFilter | |
PeptideIndexer |
This TOPP tool calculates the false discovery rate (FDR) for results of target-decoy searches. The FDR calculation can be performed for proteins and/or for peptides (more exactly, peptide spectrum matches).
The false discovery rate is defined as the number of false discoveries (decoy hits) divided by the number of false and correct discoveries (both target and decoy hits) with a score better than a given threshold.
PeptideIndexer must be applied to the search results (idXML file) to index the data and to annotate peptide and protein hits with their target/decoy status.
The command line parameters of this tool are:
FalseDiscoveryRate -- Estimates the false discovery rate on peptide and protein level using decoy searches. Version: 2.4.0 Oct 29 2018, 15:52:19, Revision: 9690d06 To cite OpenMS: Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959. Usage: FalseDiscoveryRate <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>* Identifications from searching a target-decoy database. (valid formats: 'idXML') -out <file>* Identifications with annotated FDR (valid formats: 'idXML') -PSM <FDR level> Perform FDR calculation on PSM level (default: 'true' valid: 'true', 'false') -protein <FDR level> Perform FDR calculation on protein level (default: 'true' valid: 'true', 'false') FDR control: -FDR:PSM <fraction> Filter PSMs based on q-value (e.g., 0.05 = 5% FDR, disabled for 1) (default: '1' min: '0' max: '1') -FDR:protein <fraction> Filter proteins based on q-value (e.g., 0.05 = 5% FDR, disabled for 1) (default: '1' min: '0' max: '1') 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: