Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value.
An arbitrary number of idXML files resulting from a target+decoy search can be provided as input.
Since the q-value can be computed independently from a scoring scheme, no further preprocessing (like IDPep or FDR) is required, apart from a target-decoy annotation! I.e., apply PeptideIndexer to the immediate output of a search engine (or ConsensusID) and use this as input to this tool.
The command line parameters of this tool are:
IDEvaluator -- Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifi
cations for a certain q-value.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
  IDEvaluator <options>
This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
on or use the --helphelp option.
Options (mandatory options marked with '*'):
  -in <file>             Input file(s) (valid formats: 'idXML')
  -out <file>            Output file (if given, no GUI will be displayed) (valid formats: 'png', 'jpg', 'svg'
                         )
  -out_type <file type>  The image format. Set this if you want to force a format not reflected by the 'out' 
                         filename. (valid: 'png', 'jpg', 'svg')
  -out_csv <file>        Optional output of points as table for manual post-processing. (valid formats: 'csv'
                         )
  -q_min <float>         Minimal q-value in plot. (default: '0' min: '0' max: '1')
  -q_max <float>         Maximal q-value in plot. (default: '0.4' 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)
The following configuration subsections are valid:
 - algorithm   Additional parameters for FDR and image sizes.
You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
Have a look at the OpenMS documentation for more information.
INI file documentation of this tool:
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |