Groups corresponding features from multiple maps using a QT clustering approach.
potential predecessor tools | FeatureLinkerUnlabeledQT | potential successor tools |
FeatureFinderCentroided (or another feature detection algorithm) | ProteinQuantifier | |
MapAlignerPoseClustering (or another map alignment algorithm) | TextExporter | |
SeedListGenerator |
Reference:
Weisser et al.: An automated pipeline for high-throughput label-free quantitative proteomics (J. Proteome Res., 2013, PMID: 23391308).
This tool provides an algorithm for grouping corresponding features in multiple runs of label-free experiments. For more details and algorithm-specific parameters (set in the ini file) see "Detailed Description" in the algorithm documentation".
FeatureLinkerUnlabeledQT takes several feature maps (featureXML files) and stores the corresponding features in a consensus map (consensusXML file). Feature maps can be created from MS experiments (peak data) using one of the FeatureFinder TOPP tools.
The command line parameters of this tool are:
FeatureLinkerUnlabeledQT -- Groups corresponding features from multiple maps. Version: 2.3.0 Jan 9 2018, 17:46:23, Revision: 38ae115 Usage: FeatureLinkerUnlabeledQT <options> This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript ion or use the --helphelp option. Options (mandatory options marked with '*'): -in <files>* Input files separated by blanks (valid formats: 'featureXML', 'consensusXML') -out <file>* Output file (valid formats: 'consensusXML') -design <file> Input file containing the experimental design (valid formats: 'tsv') -keep_subelements For consensusXML input only: If set, the sub-features of the inputs are transferred to the output. 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) The following configuration subsections are valid: - algorithm Algorithm parameters section 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 2.3.0 | Documentation generated on Tue Jan 9 2018 18:22:06 using doxygen 1.8.13 |