Institute for Advanced Biosciences Keio University
MathDAMP Mathematica package for differential analysis of metabolite profiles
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MathDAMP > Examples > 07-MathDAMP-Reference

07-MathDAMP-Reference

This notebook provides reference documentation for MathDAMP functions.

DAMPAlign

DAMPAlignAnnotationTable

DAMPAlignPeakList

DAMPAnnotationTableToPeakList

DAMPAppendToSampleName

DAMPApplyFunctionToGroup

DAMPApplyFunctionToSingle

DAMPBinChromatogram

DAMPCheckDir

DAMPCrop

DAMPDensityPlot

DAMPDPScore

DAMPDrawAnnotation

DAMPDropMZs

DAMPExportBDT

DAMPFilter

DAMPFitShiftFunction

DAMPGenColors

DAMPGetChromatogram

DAMPGetIntensities

DAMPGradient

DAMPGradientPalette

DAMPImportBDT

DAMPImportCDF

DAMPImportCSV

DAMPImportMS

DAMPImportMZXML

DAMPIntegrate

DAMPLoadAnnotationTable

DAMPMultiGroups

DAMPNormalize

DAMPNormalizeGroup

DAMPOutliers

DAMPParallelPlot

DAMPPeakListToAnnotationTable

DAMPPickChromatogramPeaks

DAMPPickPeaks

DAMPPlotCandidates

DAMPPlotChromatogram

DAMPPlotPeakLayout

DAMPRemoveNoise

DAMPRemoveSpikes

DAMPRobustPolynomialFit

DAMPSelectMZs

DAMPSelectRepresentativePeaks

DAMPSmooth

DAMPSubtractBaselines

DAMPThreshold

DAMPTrendFilter

DAMPTwoDatasets

DAMPTwoGroups

DAMPAlign

DAMPAlign[msdata,shiftfunction,timepoints,options] aligns msdata according to timeshift func ... om the msdata to keep track of modifications performed on the dataset (default: \"a\")

DAMPAlignAnnotationTable

DAMPAlignAnnotationTable[peaklist,annotationtable,options] aligns annotationtable to peaklis ... re binned to 0.1 m/z resolution, the resolution option should be set to 0.1 as well (default: 1)

DAMPAlignPeakList

DAMPAlignPeakList[peaklist,timeshiftfunction] applies the retention/migration time shift fun ... ration times in the peaklist (expected to have format as returned by the function DAMPPickPeaks)

DAMPAnnotationTableToPeakList

DAMPAnnotationTableToPeakList[annotationtable,options] converts an annotation table (execute ... termines to which resolution the m/z values in the annotation table will be rounded (default: 1)

DAMPAppendToSampleName

DAMPAppendToSampleName[msdata4,string] appends string to the SampleName in msdata4. msdata4  ... s separated from previous modifiers by two vertical bars with a space in between (default: True)

DAMPApplyFunctionToGroup

DAMPApplyFunctionToGroup[msdatas,function,options] applies function to either all correspond ... leName to keep the track of the modifications performed on the dataset (default: \"\")

DAMPApplyFunctionToSingle

DAMPApplyFunctionToSingle[msdata,function,options] applies a pure function function to msdat ... rom the msdata to keep track of modifications performed on the dataset (default: \"\")

DAMPBinChromatogram

DAMPBinChromatogram[chromatogram,binsize,options] bins the chromatogram by dissecting it int ...  - function to be applied to signal intensities and timepoints in every interval (default: Mean)

DAMPCheckDir

DAMPCheckDir[directory] checks if directory exists, creates it if it does not. The parent directory must exist, error message is shown otherwise.

DAMPCrop

DAMPCrop[msdata,options] reduces the msdata dataset to datapoints falling within the timeran ... fault: All)<br />TimeRange - two element list specifying the cropping time range (default: All).

DAMPDensityPlot

DAMPDensityPlot[msdata,options] plots the msdata using the ListDensityPlot function. A gradi ...  lists of options must correspond to the number of passed annotation tables (default: Automatic)

DAMPDPScore

DAMPDPScore[peaklist1,peaklist2,options] calculates the dynamic programming (DP) score betwe ... ckPeaks function.<br />Options:<br />GapPenalty - gap penalty (in minutes) for DP (default: 0.5)

DAMPDrawAnnotation

DAMPDrawAnnotation[annotationtable,options] draws the annotation for density plots. (For det ... appears to appropriately capture the dimensions of peaks on the ListDensityPlot (default: {1,1})

DAMPDropMZs

DAMPDropMZs[msdata,mzs] reduces the msdata datased by eliminating datapoints corresponding to m/z values specified in the mzs list.

DAMPExportBDT

DAMPExportBDT[filename,msdata] exports data in a MathDAMP format {matrix of signal intensiti ... egular list of m/z values which can be converted to the range representation should be exported.

DAMPFilter

DAMPFilter[msdata,criteriamsdata,threshold,options] sets to 0 those signal intensities in ms ... he msdata to keep the track of modifications performed on the dataset (default: \"f\")

DAMPFitShiftFunction

DAMPFitShiftFunction[peaklist1,peaklist2,options] optimizes the parameters of a retention/mi ... s the selection time range of peaks from peaklist1 to be used for scoring (default: {0,∞})

DAMPGenColors

DAMPGenColors[number] generates a list of color specifications with a number of elements det ... mber>6, the hue range is split proportionally and the colors are assigned from this sequence.

DAMPGetChromatogram

DAMPGetChromatogram[msdata,mz] returns a chromatogram/electropherogram (a list of {time,signal intensity} elements) from msdata corresponding to m/z mz.

DAMPGetIntensities

DAMPGetIntensities[msdata,mz] returns a list of signal intensities from msdata corresponding to m/z mz.

DAMPGradient

DAMPGradient[pos1,pos2,color1,color2,backgroundgraylevel] returns a function which calculate ... 0;1>) at pos1, and color2 at pos2, and finally to darkened color2 at the relative position 1.

DAMPGradientPalette

DAMPGradientPalette[options] - generates a color palette for assigning colors to intensity v ... gative range color gradients, palette entry for value 0 is shared between the two (default: 100)

DAMPImportBDT

DAMPImportBDT[filename,samplename] reads and processes a binary BDT file specified by filena ...  information about the sample name, this has to be specified as a second parameter (samplename).

DAMPImportCDF

DAMPImportCDF[filename,options] reads and processes a CDF file specified by filename into a  ... tion - specifies the resolution to which the data will be binned along the m/z axis (default: 1)

DAMPImportCSV

DAMPImportCSV[filename,samplename,options] reads and processes a csv file generated by Analy ... tion along with current time every 100 processed chromatograms/electropherograms (default: True)

DAMPImportMS

DAMPImportMS[filename] reads and processes an Agilent ChemStation MS file specified by filen ... rsal for SIM and scan mode datafiles. The data are binned to 1 m/z unit resolution by averaging.

DAMPImportMZXML

DAMPImportMZXML[filename,samplename,options] reads and processes the first level MS scans fr ...  is recommended for scan data, Selective mode is recommended for SIM data. (default: Sequential)

DAMPIntegrate

DAMPIntegrate[chromatogram,options] calculates the area below the signal intensities of a ch ... elineFromTimeRange (default: None). If set to None, baseline is set to signal intensity value 0.

DAMPLoadAnnotationTable

DAMPLoadAnnotationTable[filename] loads a list of annotation labels for plots from a csv fil ... y plots relative to the label (1 - right, 2 - top, 3 - left, 4 - bottom, 1.5 - top right, etc.).

DAMPMultiGroups

DAMPMultiGroups[msdatas,replicates,options] performs the comparison of multiple groups of da ...  to Automatic, the SampleName of the first dataset from every group is used (default: Automatic)

DAMPNormalize

DAMPNormalize[msdata,coefficient,options] multiplies the signal intensities in msdata (msdat ... he msdata to keep the track of modifications performed on the dataset (default: \"n\")

DAMPNormalizeGroup

DAMPNormalizeGroup[msdatas,options] aligns msdatas (a list of datasets) and normalizes them  ...  signal intensities are rounded to integers in internal calculations and results (default: True)

DAMPOutliers

DAMPOutliers[msdatas,options] highlights the presence of outlying signal intensities in msda ... ill be generated for every dataset in msdatas in addition to the overall result (default: False)

DAMPParallelPlot

DAMPParallelPlot[msdatas,options] plots msdatas (a list of datasets) on a density plot in a  ...  passed directly to the DAMPDensityPlot function which is used internally for plotting the data.

DAMPPeakListToAnnotationTable

DAMPPeakListToAnnotationTable[peaklist,options] converts the peaklist returned by DAMPPickPe ...  - specifies the position of the text label relative to the annotation label mark (default: 1.5)

DAMPPickChromatogramPeaks

DAMPPickChromatogramPeaks[chromatogram,options] picks peaks from chromatogram and returns th ... k-top strategic point for the calculation of centroided retention/migration time (default: 0.05)

DAMPPickPeaks

DAMPPickPeaks[msdata,options] picks peaks from all chromatograms/electropherograms in msdata ... function which is used internally to pick peaks from individual chromatograms/electropherograms.

DAMPPlotCandidates

DAMPPlotCandidates[msdatas,criteriamsdata,options] plots a ranked list of overlaid chromatog ... gram function which is used internally to plot the chromatograms/electropherograms (default: {})

DAMPPlotChromatogram

DAMPPlotChromatogram[{msdata,msdata,...},mz,options] plots multiple overlaid chromatograms/e ...  Automatic is specified, the SampleName from each msdata is used as a label (default: Automatic)

DAMPPlotPeakLayout

DAMPPlotPeakLayout[peaklists,options] plots the positions of peaks from a list of peaklists  ... #62754;False],PlotSymbol[Diamond,3,FilledFalse],PlotSymbol[Box,3,FilledFalse]}})

DAMPRemoveNoise

DAMPRemoveNoise[msdata,options] removes noise from every chromatogram/electropherogram in ms ... e msdata to keep the track of modifications performed on the dataset (default: \"nr\")

DAMPRemoveSpikes

DAMPRemoveSpikes[msdata,options] levels to 0 all signal intensity values both neighbours of  ... e msdata to keep the track of modifications performed on the dataset (default: \"sr\")

DAMPRobustPolynomialFit

DAMPRobustPolynomialFit[chromatogram,options] fits a polynomial to chromatogram data by robu ... one not to bin the data for polynomial fitting (default: (DAMPBinChromatogramFast[#,0.25]&))

DAMPSelectMZs

DAMPSelectMZs[msdata,mzs] reduces the msdata datased to datapoints corresponding to m/z values specified in the mzs list.

DAMPSelectRepresentativePeaks

DAMPSelectRepresentativePeaks[peaklist,options] reduces the peaklist returned by the DAMPPic ... t: 1)<br />TimeRange - select peaks from this retention/migration time range only (default: All)

DAMPSmooth

DAMPSmooth[msdata,options] applies a smoothing function to all chromatograms/electropherogra ... om the msdata to keep track of modifications performed on the dataset (default: \"s\")

DAMPSubtractBaselines

DAMPSubtractBaselines[msdata,options] subtracts baselines from all chromatograms/electropher ... e msdata to keep the track of modifications performed on the dataset (default: \"bs\")

DAMPThreshold

DAMPThreshold[msdata,threshold,options] levels to 0 all signal intensity values in msdata wh ... om the msdata to keep track of modifications performed on the dataset (default: \"t\")

DAMPTrendFilter

DAMPTrendFilter[group1msdatas,group2msdatas,tofiltermsdata,filtnum,options] filters out thos ... ermsdata to keep the track of modifications performed on the dataset (default: \"tf\")

DAMPTwoDatasets

DAMPTwoDatasets[msdata1,msdata2,options] generates datasets representing the absolute, relat ... al intensities from msdata1 and msdata2 are equal to or greater than this threshold (default: 0)

DAMPTwoGroups

DAMPTwoGroups[msdatas1,msdatas2,options] generates datasets representing the absolute, relat ... is is intended to filter out results originating from individual spikes or outliers (default: 2)