XFDR

Calculates false discovery rate estimates on crosslink identifications.

This tool calculates and FDR estimate for crosslink identifications, which are produced by OpenPepXL. The method employed currently is identical to the target-decoy approach used by xProphet (Walzthoeni et al., 2012). Consequently, this tool can also consume xquest.xml files (produced either by OpenPepXL or xQuest). The tool supports output in the idXML and mzIdentML formats.

Experimental classes:: This tool is work in progress and usage and input requirements might change.

pot. predecessor tools	$\longrightarrow$ XFDR $\longrightarrow$	pot. successor tools
OpenPepXL		OpenPepXLLF	-

The command line parameters of this tool are:

XFDR -- Calculates false discovery rate estimates on crosslink identifications
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

Usage:
  XFDR <options>

Options (mandatory options marked with '*'):
  -in <file>                        Crosslink Identifications in either xquest.xml, idXML, or mzIdentML forma
                                    t (as produced by OpenPepXL) (valid formats: 'xml', 'idXML', 'mzid')
  -in_type <in_type>                Type of input file provided with -in (valid: 'xml', 'idXML', 'mzid')
  -out_idXML <idXML_file>           Output as idXML file (valid formats: 'idXML')
  -out_mzIdentML <mzIdentML_file>   Output as mzIdentML file (valid formats: 'mzid')
  -minborder <minborder>            Filter for minimum precursor mass error (ppm). Can only be applied for 
                                    xquest.xml input. (default: '-1')
  -maxborder <maxborder>            Filter for maximum precursor mass error (ppm). Can only be applied for 
                                    xquest.xml input. (default: '-1')
  -mindeltas <mindeltas>            Filter for delta score, 0 is no filter. Minimum delta score required, 
                                    hits are rejected if larger or equal. Can only be applied for xquest.xml
                                    input. (default: '0' min: '0' max: '1')
  -minionsmatched <minionsmatched>  Filter for minimum matched ions per peptide. Can only be applied for xque
                                    st.xml input. (default: '0' min: '0')
  -uniquexl                         Calculate statistics based on unique IDs. Can only be applied for xquest.
                                    xml input.
  -no_qvalues                       Do not transform simple FDR to q-values
  -minscore <minscore>              Minimum score to be considered for FDR calculation (default: '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

+XFDRCalculates false discovery rate estimates on crosslink identifications

version2.3.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'XFDR'

in Crosslink Identifications in either xquest.xml, idXML, or mzIdentML format (as produced by OpenPepXL)input file*.xml,*.idXML,*.mzid

in_type Type of input file provided with -inxml,idXML,mzid

out_idXML Output as idXML fileoutput file*.idXML

out_mzIdentML Output as mzIdentML fileoutput file*.mzid

minborder-1 Filter for minimum precursor mass error (ppm). Can only be applied for xquest.xml input.

maxborder-1 Filter for maximum precursor mass error (ppm). Can only be applied for xquest.xml input.

mindeltas0 Filter for delta score, 0 is no filter. Minimum delta score required, hits are rejected if larger or equal. Can only be applied for xquest.xml input.0:1

minionsmatched0 Filter for minimum matched ions per peptide. Can only be applied for xquest.xml input.0:∞

uniquexlfalse Calculate statistics based on unique IDs. Can only be applied for xquest.xml input.true,false

no_qvaluesfalse Do not transform simple FDR to q-valuestrue,false

minscore0 Minimum score to be considered for FDR calculation

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