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:

for a single chemical shift query (e.g. 3.136), database=metabolomics >> “http://webapi.bmrb.wisc.edu/v2/search/multiple_shift_search?s=3.136&database=metabolomics”

for multiple chemical shift searches (e.g. 3.136,7): >> “http://webapi.bmrb.wisc.edu/v2/search/multiple_shift_search?s=3.136&s=7.0&database=metabolomics”

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]¶