Built-in Configuration SOPs

The following tables list, define and give default values for all of the SOP parameters for each method.

All Dataset Objects

Required SOP parameters for all Dataset objects
Key Type Default value Role
‘noFiles’ int 10 When showing a ranked list of files show only the top/bottom noFiles
‘dpi’ int 300 Raster resolution when plotting figures
‘figureSize’ list of float [11,7] Size to plot figures
‘figureFormat’ str ‘png’ Format to save figures in
‘histBins’ int 100 Number of bins to use when drawing histograms
‘quantiles’ list of float [25, 75] When calculating percentiles, use this default range
Optional SOP parameters for all Dataset objects
Key Type Default value Role
‘analyticalMeasurements’ dict {} Set of key, value pairs where each key is a column in sampleMetadata and the value is ‘categorical’ or ‘continuous’ depending on parameter type. Columns described here will be checked for association in the multivariate quality control reports when run with the analytical setting.
‘excludeFromPlotting’ list of str [] Column names in sampleMetadata to exclude from plotting
‘sampleMetadataNotExported’ list of str [“Exclusion Details”] Column names in sampleMetadata to exclude from data export
‘featureMetadataNotExported’ list of str [] Column names in featureMetadata to exclude from data export

MSDataset Objects

SOP parameters for all MSDataset objects
Parameter Type Default value Role
‘corrThreshold’ float 0.7 When filtering features by correlation to dilution using the Serial Dilution Sample, the correlation must be above this
‘corrMethod’ str ‘pearson’ Type of correlation to linearity to calculate, must be ‘pearson’ or ‘spearman’
‘rsdThreshold’ float 30 When filtering features by RSD, the RSD must be below this
‘varianceRatio’ float 1.1 When filtering features RSD in Study Samples must be at least RSD in Precision Reference * this value
‘blankThreshold’ float 1.1 When filtering features RSD in Study Samples must be at least RSD in Procedural Blank samples * this value
‘artifactualFilter’ str (bool) ‘False’ Flag for whether artifactual filtering should be applied when filtering features
‘deltaMzArtifactual’ float 0.1 ‘artifactualFilter’ parameter: Maximum allowed m/z distance between two grouped features
‘overlapThresholdArtifactual’ int 50 ‘artifactualFilter’ parameter: Minimum peak overlap between two grouped features
‘corrThresholdArtifactual’ float 0.9 ‘artifactualFilter’ parameter: Minimum correlation between two grouped features
‘filenameSpec’ str (regex) see ‘GenericMS.json’ Regular expression to pull out information from raw MS data filenames (as per NPC standard naming conventions)

NMRDataset Objects

SOP parameters for all NMRDataset objects
Parameter Type Default value (for GenericNMRUrine) Default value (for GenericNMRBlood) Role
‘bounds’ list of float [-1, 10] [-1, 10] Region of the original spectrum to re-interpolate and retain
‘variableSize’ int 20000 20000 Number of points in the re-interpolated spectrum
‘alignTo’ str ‘singlet’ ‘doublet’ Type of signal to calibrate to
‘calibrateTo’ float 0 5.233 Chemical shift value to calibrate to
‘ppmSearchRange’ list of float [-0.3, 0.3] [4.9, 5.733] Chemical shift region to search for calibration signal
‘LWpeakMultiplicity’ str ‘singlet’ ‘quartet’ Type of signal used to measure line width
‘LWpeakRange’ list of float [-0.1, 0.1] [4.08, 4.14] Chemical shift region to search for line width signal
‘LWFailThreshold’ float 1.3 1.3 Line-width check cut-off in Hz
‘baselineCheckRegion’ list of list pairs of floats [[-2, -0.5], [9.5, 12.5]] [[-2, -0.5], [9.5, 12.5]] Chemical shift regions to use in baseline quality checks
‘solventPeakCheckRegion’ list of list pairs of floats [[4.6, 4.7],[4.9,5]] [[4.4, 4.5], [4.85,5]] Chemical shift regions to use in water suppression quality checks
‘exclusionRegions’ list of list pairs of floats [[-0.2,0.2],[4.7,4.9]] [[-0.2,0.2],[4.5,4.85]] Chemical shift regions to mark for exclusion by default during pre-processing