ccpn.AnalysisMetabolomics.lib package

Submodules

ccpn.AnalysisMetabolomics.lib.BMRBquery module

Module Documentation here

ccpn.AnalysisMetabolomics.lib.BMRBquery.ShiftColumns = ['Assigned_chem_shift_list_ID', 'Combined_offset', 'Entry_ID', 'Link', 'Peaks_matched', 'Title']

Full address to be:

ccpn.AnalysisMetabolomics.lib.BMRBquery.bmrbMultiShiftSearch(shifts: list, databaseType='metabolomics')[source]
ccpn.AnalysisMetabolomics.lib.BMRBquery.peaksToShifts1D(objs)[source]
Parameters

objs – peaks or multiplets

Returns

a list of peak positions

ccpn.AnalysisMetabolomics.lib.BMRBquery.testAla()[source]

ccpn.AnalysisMetabolomics.lib.centering module

ccpn.AnalysisMetabolomics.lib.centering.meanCenter(spectrumCluster)[source]
ccpn.AnalysisMetabolomics.lib.centering.medianCenter(spectrumCluster)[source]

ccpn.AnalysisMetabolomics.lib.commands module

class ccpn.AnalysisMetabolomics.lib.commands.Command(method, methodSpec, how)[source]

Bases: object

add(targetSpec)[source]
divide(targetSpec)[source]
multiply(targetSpec)[source]
process(targetSpec)[source]
subtract(targetSpec)[source]
unprocess(targetSpec)[source]

ccpn.AnalysisMetabolomics.lib.decomposition module

class ccpn.AnalysisMetabolomics.lib.decomposition.PCA(dataFrame, nComponents=None, confidenceLimit=0.95)[source]

Bases: object

property confidenceLimit

- None, mutable -

property confidenceLimits_

- None, immutable -

property eigenvalues_

- None, immutable -

property explainedVariance_

- None, immutable -

property loadings_

- None, immutable -

property nComponents

- None, mutable -

property predictions_

- None, immutable -

property qConfLimit

- None, immutable - From: J. Edward Jackson and Govind S. Mudholkar Technometrics Vol. 21, No. 3 (Aug., 1979), pp. 341-349 http://www.jstor.org/stable/1267757?seq=1#page_scan_tab_contents :return:

property qScores_

- None, immutable -

property residualEigenvalues_

- None, immutable -

property residuals_

- None, immutable -

property scores_

- None, immutable -

property t2ConfLimit

- None, immutable - from http://users.stat.umn.edu/~gary/classes/5401/handouts/11.hotellingt.handout.pdf

property t2Scores_

- None, immutable -

ccpn.AnalysisMetabolomics.lib.normalisation module

ccpn.AnalysisMetabolomics.lib.normalisation.getSpectrumCluster(spectra)[source]
ccpn.AnalysisMetabolomics.lib.normalisation.pqn(spectrumCluster)[source]
ccpn.AnalysisMetabolomics.lib.normalisation.tsa(spectra)[source]
ccpn.AnalysisMetabolomics.lib.normalisation.updateSpectrumCluster(spectra, spectrumCluster)[source]

ccpn.AnalysisMetabolomics.lib.persistence module

class ccpn.AnalysisMetabolomics.lib.persistence.Borg[source]

Bases: object

class ccpn.AnalysisMetabolomics.lib.persistence.MetabolomicsPersistenceDict(*args, **kwargs)[source]

Bases: collections.OrderedDict

instance = None
ccpn.AnalysisMetabolomics.lib.persistence.bruker1dDict(refDF=None, SF=1, FTSIZE=None, SW_p=None, OFFSET=None)[source]
ccpn.AnalysisMetabolomics.lib.persistence.spectraDicToBrukerExperiment(spectraDF, directoryName, **kwargs)[source]
ccpn.AnalysisMetabolomics.lib.persistence.writeBruker(directory, dic, data)[source]

ccpn.AnalysisMetabolomics.lib.pipeline module

ccpn.AnalysisMetabolomics.lib.pipeline.pipeline(spectra, commands)[source]

ccpn.AnalysisMetabolomics.lib.scaling module

ccpn.AnalysisMetabolomics.lib.scaling.autoScale(spectra)[source]
ccpn.AnalysisMetabolomics.lib.scaling.levelScale(spectra)[source]
ccpn.AnalysisMetabolomics.lib.scaling.paretoScale(spectra)[source]
ccpn.AnalysisMetabolomics.lib.scaling.rangeScale(spectra)[source]
ccpn.AnalysisMetabolomics.lib.scaling.unitVarianceScale(spectra)[source]
ccpn.AnalysisMetabolomics.lib.scaling.varianceScale(spectrumCluster, power)[source]
ccpn.AnalysisMetabolomics.lib.scaling.vastScale(spectra)[source]

ccpn.AnalysisMetabolomics.lib.transformations module

Module documentation here.

ccpn.AnalysisMetabolomics.lib.transformations.logTransform(spectrumCluster)[source]
ccpn.AnalysisMetabolomics.lib.transformations.powerTransform(spectrumCluster, power=0.5)[source]