FFEval

Evaluation tool for feature detection algorithms.

To plot the ROC curve you might use:

d = read.table("data.roc", skip=1, sep="\t")
plot(d[,3],d[,4], xlim=c(0,1),ylim=c(0,1), xlab="FDR",ylab="TPR",main="ROC with varying intensity")
lines(c(0,1),c(0,1))

The command line parameters of this tool are:

FFEval -- Evaluation tool for feature detection algorithms.
Full documentation: http://www.openms.de/doxygen/release/3.0.0/html/UTILS_FFEval.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:
  FFEval <options>

Options (mandatory options marked with '*'):
  -in <file>*            Feature input file, which contains the data to be tested against the truth file. 
                         (valid formats: 'featureXML')
  -truth <file>*         Truth feature file that defines what features should be found. (valid formats: 'feat
                         ureXML')
  -rt_tol <double>       Allowed tolerance of RT relative to average feature RT span. (default: '0.3') (min: 
                         '0.0')
  -rt_tol_abs <double>   Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero). (default: 
                         '-1.0') (min: '-1.0')
  -mz_tol <double>       Allowed tolerance in m/z (is divided by charge). (default: '0.25') (min: '0.0')
  -out <file>            Feature output file. If given, an annotated input file is written. (valid formats: 
                         'featureXML')
  -abort_reasons <file>  Feature file containing seeds with abort reasons. (valid formats: 'featureXML')
  -out_roc <file>        If given, a ROC curve file is created (ROC points based on intensity threshold) (val
                         id formats: 'csv')
                         
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

+FFEvalEvaluation tool for feature detection algorithms.

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

++1Instance '1' section for 'FFEval'

in Feature input file, which contains the data to be tested against the truth file.input file*.featureXML

truth Truth feature file that defines what features should be found.input file*.featureXML

rt_tol0.3 Allowed tolerance of RT relative to average feature RT span.0.0:∞

rt_tol_abs-1.0 Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero).-1.0:∞

mz_tol0.25 Allowed tolerance in m/z (is divided by charge).0.0:∞

out Feature output file. If given, an annotated input file is written.output file*.featureXML

abort_reasons Feature file containing seeds with abort reasons.input file*.featureXML

out_roc If given, a ROC curve file is created (ROC points based on intensity threshold)output file*.csv

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