| OpenMS 2.5.0

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/documentation/UTILS_RTEvaluation.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    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: '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: '0.0' 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
+RTEvaluation Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'RTEvaluation'
in Input file input file*.idXML
sequences_file Fasta File input file*.fasta
out Output file output file*.csv
latex false Indicates whether the output file format of the table should be LaTeX or CSV (default)true,false
p_value_dim_1 0.01 Significance level of first dimension RT filter 0.0:1.0
p_value_dim_2 0.05 Significance level of second dimension RT filter 0.0:1.0
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false