OpenMS
2.5.0
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Evaluation tool for feature detection algorithms.
To plot the ROC curve you might use:
The command line parameters of this tool are:
FFEval -- Evaluation tool for feature detection algorithms. Full documentation: http://www.openms.de/documentation/UTILS_FFEval.html Version: 2.5.0-nightly-2020-03-06 Mar 7 2020, 01:22:16, Revision: 84b1398 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: FFEval <options> Options (mandatory options marked with '*'): -in <file>* Feature input file, which contains the data to be tested against the truth file. (valid formats: 'featureXML') -truth <file>* Truth feature file that defines what features should be found. (valid formats: 'feat ureXML') -rt_tol <double> Allowed tolerance of RT relative to average feature RT span. (default: '0.3' min: '0.0') -rt_tol_abs <double> Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero). (default: '-1.0' min: '-1.0') -mz_tol <double> Allowed tolerance in m/z (is divided by charge). (default: '0.25' min: '0.0') -out <file> Feature output file. If given, an annotated input file is written. (valid formats: 'featureXML') -abort_reasons <file> Feature file containing seeds with abort reasons. (valid formats: 'featureXML') -out_roc <file> If given, a ROC curve file is created (ROC points based on intensity threshold) (val id formats: 'csv') 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)
INI file documentation of this tool: