RTEvaluation

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 idXML must have been annotated with protein sequences (for the positive hits) using PeptideIndexer. This tool then evaluates the true positives, false positives, true negatives, and false negatives 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 your LaTeX manuscripts).

Note

Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

RTEvaluation -- Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with 
predicted RTs.
Full documentation: http://www.openms.de/doxygen/release/3.0.0/html/UTILS_RTEvaluation.html
Version: 3.0.0 Jul 14 2023, 11:57:33, Revision: be787e9
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:
  RTEvaluation <options>

Options (mandatory options marked with '*'):
  -in <file>*             Input file (valid formats: 'idXML')
  -sequences_file <file>  Fasta File (valid formats: 'fasta')
  -out <file>*            Output file  (valid formats: 'tsv')
  -latex                  Indicates whether the output file format of the table should be LaTeX or TSV (defau
                          lt)
  -p_value_dim_1 <float>  Significance level of first dimension RT filter (default: '0.01') (min: '0.0' max: 
                          '1.0')
  -p_value_dim_2 <float>  Significance level of second dimension RT filter (default: '0.05') (min: '0.0' max:
                           '1.0')
                          
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:

Legend:

required parameter

advanced parameter

+RTEvaluationApplication that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.

version3.0.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'RTEvaluation'

in Input fileinput file*.idXML

sequences_file Fasta Fileinput file*.fasta

out Output file output file*.tsv

latexfalse Indicates whether the output file format of the table should be LaTeX or TSV (default)true, false

p_value_dim_10.01 Significance level of first dimension RT filter0.0:1.0

p_value_dim_20.05 Significance level of second dimension RT filter0.0:1.0

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue, false

forcefalse Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false