Available Fragment Commands

Currently, the following FragmentCommands are available for execution within the pipeline. Other FragmentCommands may be available, but have not yet been finalized for description in this file.

maltcms.commands.fragments.preprocessing.

  • TICPeakFinder : Finds well conserved peaks in the TIC
  • DenseArrayProducer : produces evenly binned intensity profiles
  • DefaultVarLoader : loads default variables

maltcms.commands.fragments.io.

  • ANDIChromImporter : import for AIA/AndiChrom files
  • ANDIMSExporter : export to AIA/ANDIMS files
  • CSVAnchorReader : read anchors in csv format
  • ObiWarplmataExporter : export profile matrices to ObiWarp's lmata format
  • VariableDataExporter : exports selected variables to csv files

maltcms.commands.fragments.cluster.

  • PairwiseDistanceCalculator : calculates pairwise distances/similarities between chromatograms
  • CompleteLinkageAlgorithm : applies CompleteLinkage based on pairwise distances
  • NeighborJoinAlgorithm : applies NeighborJoining
  • SingleLinkageAlgorithm : applies SingleLinkage
  • UPGMAAlgorithm : applies UPGMA (AverageLinkage)

maltcms.commands.fragments.assignment.

  • PeakCliqueAssignment : assigns peaks to cliques based on ms similarity, rt deviation and a bidirectional best hits criterion
  • EIMSMDBetaboliteAssignment : assigns peaks with possibly multiple matches against a MetaboliteDB instance with cosine score criterion

maltcms.commands.fragments.alignment.

  • CenterStarAlignment : selects the chromatogram with smallest overall distance to other chroms as alignment reference
  • ProgressiveTreeAlignment : generates a consensus, time corrected chromatogram as alignment reference

maltcms.commands.fragments.visualization.

  • Array1DVisualizer : visualize 1D data, e.g. TICs
  • ChromatogramVisualizer : visualize chromatograms as heatmaps
  • MZIDistributionVisualizer : visualize distribution of m/z values as histogram
  • PairwiseAlignmentMatrixVisualizer : visualize pairwise alignment matrix
  • PairwiseAlignmentVisualizer : visualize pairwise alignments
  • ScoreDistributionVisualizer : visualize score distribution histogram

maltcms.commands.fragments2d.preprocessing

  • Data2DNormalizer : normalization and filtering of 2D TIC data
  • ModulationExtractor : extracts slices of 2D GCxGC-MS data
  • GCGCToGCMSConverter : resamples 2D GCxGC-MS data to GC-MS data by integrating modulations

maltcms.commands.fragments2d.visualization

  • Chromatogram2DVisualizer : 2D heatmap visualization of 2D TIC data

maltcms.commands.fragments2d.warp

  • Variants of Dynamic Time Warping for alignment of 2D TIC data

maltcms.commands.fragments2d.warp.visualization

  • Visualizations for Dynamic Time Warping alignments of 2D TIC data

maltcms.commands.fragments2d.peakfinding

  • SeededRegionGrowing : locates and integrates 2D-TIC peaks in GCxGC-MS data, performs putative database identification and multiple peak alignment