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.
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:
  RTEvaluation <options>

Options (mandatory options marked with '*'):
  -in <file>*             Input file (valid formats: 'idXML')
  -out <file>*            Output file  (valid formats: 'csv')
  -latex                  Indicates whether the output file format of the table should be LaTeX or CSV (defau
                          lt)
  -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:

Legend:

required parameter

advanced parameter

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

version2.4.0 Version of the tool that generated this parameters file.

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

in Input fileinput file*.idXML

out Output file output file*.csv

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

p_value_dim_10.01 Significance level of first dimension RT filter0:1

p_value_dim_20.05 Significance level of second dimension RT filter0:1

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 Overwrite tool specific checks.true,false

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