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 |