PeakCliqueAlignment

Variables

var.scan_acquisition_time
var.mass_values
var.intensity_values
var.scan_index

var.binned_mass_values
var.binned_intensity_values
var.binned_scan_index
var.tic_peaks
var.eic_peaks
var.first_column_elution_time
var.second_column_elution_time
var.peak_area
var.peak_index_list
var.anchors.retention_scans
var.anchors.retention_index_names

var.anchors.retention_index_names
var.anchors.retention_times
var.anchors.retention_indices
var.anchors.retention_scans

Configurable Properties

Name: maxBBHErrors
Default Value: 0
Description:
Deprecated. Parameter will be ignored. Use minBbhFraction instead.

Name: minBbhFraction
Default Value: 1.0
Description:
Fraction of peaks in a potential cluster required to be considered valid. 1.0 means, that all peaks must be bidirectional-best hits of each other. The clusters then correspond to true cliques. Lower values will allow incomplete bidirectional-best hits. Use lower values, if the group membership criterion is too strict and leads to exclusion of too many peaks. Inspect output for number of incompatible peaks, to observe the effect. May increase the number of false positives.

Name: minCliqueSize
Default Value: -1
Description:
Minimum clique size parameter. Controls the minimum number of peaks in a clique to be reported by the alignment. If set to -1, only complete cliques will be reported.

Name: peakFactory
Default Value: Peak1DMSFactory(massesVar=mass_values, scanIndexVar=scan_index, intensitiesVar=intensity_values, binnedScanIndexVar=binned_scan_index, binnedMassesVar=binned_mass_values, binnedIntensitiesVar=binned_intensity_values, scanAcquisitionTimeVar=scan_acquisition_time)
Description:
Use a custom peak factory, use Peak1DFactory for 1D data without MS, Peak1DMSFactory for 1D data with MS, or Peak2DMSFactory for 2D data with MS.

Name: postProcessCliques
Default Value: false
Description:
Deprecated. Use minBbhFraction instead.

Name: rtNormalizationFactor
Default Value: 0.016666666666666666
Description:
Sets the retention time normalization factor for multiple peak alignment output of retention times. The factor is multiplied with the native retention time of each peak.

Name: rtOutputFormat
Default Value: 0.000
Description:
Output format for retention times. Default has three trailing decimal places: “0.000” .

Name: saveIncompatiblePeaks
Default Value: false
Description:
If true, save incompatible peaks in msp compatible format.

Name: savePeakMatchAreaPercentTable
Default Value: true
Description:
If true, stores multiple alignment file with percentage of peak areas.

Name: savePeakMatchAreaTable
Default Value: true
Description:
If true, stores multiple alignment file with peak areas.

Name: savePeakMatchRTTable
Default Value: true
Description:
If true, stores multiple alignment file with 1D peak retention times.

Name: savePeakSimilarities
Default Value: false
Description:
If true, stores peak similarities for every pairwise similarity calculation. May create a large number of output files (quadratic in number of chromatograms).

Name: savePlots
Default Value: false
Description:
If true, save plots of cliques and of One-Way Anova and F-Test results.

Name: saveUnassignedPeaks
Default Value: false
Description:
If true, save unassigned peaks in msp compatible format.

Name: saveUnmatchedPeaks
Default Value: false
Description:
If true, save unmatched peaks in msp compatible format.

Name: saveXMLAlignment
Default Value: true
Description:
If true, stores the multiple alignment in Maltcms XML alignment format.

Name: use2DRetentionTimes
Default Value: false
Description:
Deprecated, use a Peak2DMSFactory to use 2D retention times for peaks

Name: useSparseArrays
Default Value: false
Description:
If true, use sparse mass spectra instead of binned ones. May reduce memory footprint, but will increase runtime.

Name: useUserSuppliedAnchors
Default Value: false
Description:
If true, will check for user supplied anchors and use them to augment other peak data, as provided by e.g. tic_peaks, eic_peaks, or peak_index_list.Requires upstream command to provide var.anchors.retention_scans and var.anchors.retention_names.If false, no user-supplied anchors will be used.

Name: workerFactory
Default Value: WorkerFactory(maxRTDifference=60.0, similarityFunction=ProductSimilarity(scalarSimilarities=[GaussianDifferenceSimilarity(tolerance=5.0, threshold=0.0)], arraySimilarities=[ArrayCorr{}]), assumeSymmetricSimilarity=false, savePeakSimilarities=false)
Description:
Use a custom worker factory, use WorkerFactory for 1D data, Worker2DFactory for 2D data.