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Map alignment

OpenMS offers a number of map alignment algorithms. The take several peak or feature maps and transform the retention time axis so that peak/feature positions become comparable.

The classes described in this section can be found in the ANALYSIS/MAPMATCHING folder.

All map alignment algorithms are derived from the common base class MapAlignmentAlgorithm and, thus, share a common interface. That is why only one example (Tutorial_MapAlignment.C) is shown here. Other algorithms can be work accordingly.

First, we load two feature maps:

Int main()
{
vector<FeatureMap<> > maps;
maps.resize(2);
FeatureXMLFile xml_file;
xml_file.load("data/Tutorial_MapAlignment_1.featureXML",maps[0]);
xml_file.load("data/Tutorial_MapAlignment_2.featureXML",maps[1]);

Then, we instanciate the algorithm and align the feature maps:

MapAlignmentAlgorithmPoseClustering algorithm;
// ... set parameters
vector<TransformationDescription> transformations;
algorithm.alignFeatureMaps(maps,transformations);

Finally, the aligned maps are written to files:

xml_file.store("output/Tutorial_MapAlignment_1.featureXML",maps[0]);
xml_file.store("output/Tutorial_MapAlignment_2.featureXML",maps[1]);
return 0;
} //end of main
As an additional output the algorithms return one TransformationDescription per input file. This TransformationDescription describes the transformation that was applied to the retention times.

Note
In order to align peak maps the method alignPeakMaps has to be used.

OpenMS / TOPP release 1.9.0 Documentation generated on Sun Oct 27 2013 01:11:37 using doxygen 1.8.4