Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
ConsensusMapNormalizer

Normalization of intensities in a set of maps using robust regression.

potential predecessor tools $ \longrightarrow $ ConsensusMapNormalizer $ \longrightarrow $ potential successor tools
FeatureLinkerUnlabeled
(or another feature grouping tool)
ProteinQuantifier
TextExporter

The tool normalizes the intensities of a set of maps (consensusXML file). The following normalization algorithms are available:

The command line parameters of this tool are:

ConsensusMapNormalizer -- Normalizes maps of one consensusXML file
Version: 2.0.0 Aug 19 2015, 22:19:33, Revision: GIT-NOTFOUND

Usage:
  ConsensusMapNormalizer <options>

Options (mandatory options marked with '*'):
  -in <file>*               Input file (valid formats: 'consensusXML')
  -out <file>*              Output file (valid formats: 'consensusXML')
                            
  -algorithm_type <type>    The normalization algorithm that is applied. (default: 'robust_regression' valid:
                            'robust_regression', 'median', 'quantile')
  -ratio_threshold <ratio>  Only for 'robust_regression': the parameter is used to distinguish between non-ou
                            tliers (ratio_threshold < intensity ratio < 1/ratio_threshold) and outliers. (def
                            ault: '0.67' min: '0.001' max: '1')
                            
Common TOPP 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
+ConsensusMapNormalizerNormalizes maps of one consensusXML file
version2.0.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'ConsensusMapNormalizer'
in input fileinput file*.consensusXML
out output fileoutput file*.consensusXML
algorithm_typerobust_regression The normalization algorithm that is applied.robust_regression,median,quantile
ratio_threshold0.67 Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold < intensity ratio < 1/ratio_threshold) and outliers.0.001:1
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

OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:31 using doxygen 1.8.9.1