Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
The method needs an idXML file with IDs and predicted RTs. The second input file is a file containing the protein sequences which are considered as positive hits. This tool then evaluates the tps, fps, tns, and fns for the unfiltered IDs, for the IDs filtered in first RT dimension, for the IDs filtered in the second RT dimension as well as for the IDs filtered in both dimensions. The output is a table with either csv format (can be imported by Excel) or latex format (to include in tables in your latex manuscripts).
RTEvaluation -- Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs. Version: 2.0.0 Aug 19 2015, 22:19:33, Revision: GIT-NOTFOUND Usage: RTEvaluation <options> Options (mandatory options marked with '*'): -in <file>* Input file (valid formats: 'idXML') -out <file>* Output file (valid formats: 'csv') -sequences_file <file> Filename of a FASTA file containing protein sequences. All peptides that are not a substring of a sequence in this file are considered as false (valid formats: 'fasta') -latex Indicates whether the output file format of the table should be latex or csv -p_value_dim_1 <float> Significance level of first dimension RT filter (default: '0.01' min: '0' max: '1') -p_value_dim_2 <float> Significance level of second dimension RT filter (default: '0.05' min: '0' max: '1') 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:
OpenMS / TOPP release 2.0.0 | Documentation generated on Thu Aug 20 2015 01:44:32 using doxygen 1.8.9.1 |