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 |