Institute for Advanced Biosciences Keio University
MathDAMP Mathematica package for differential analysis of metabolite profiles
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MathDAMP > Examples > MathDAMP source > Usage Description Section

Usage Description Section

This section contains a list of explanations for MathDAMP's public functions. This information is shown upon executing the ?FunctionName in any notebook after loading the MathDAMP package.

DAMPStrInternalFormat = "{matrix of signal intensities, list of m/z values, list of timepoints, additional information (list of rules)}"

DAMPStrResolution = "specifies the resolution to which the data will be binned along the m/z axis"

DAMPImportMS :: usage = DAMPImportMS[filename] reads and processes an Agilent ChemStation MS ... nd scan mode datafiles. The data are binned to 1 m/z unit resolution by averaging."

DAMPImportCSV :: usage = DAMPImportCSV[filename,samplename,options] reads and processes a cs ... h current time every 100 processed chromatograms/electropherograms (default: True)"

DAMPImportMZXML :: usage = DAMPImportMZXML[filename,samplename,options] reads and processes  ... d for scan data, Selective mode is recommended for SIM data. (default: Sequential)"

DAMPImportCDF :: usage = DAMPImportCDF[filename,options] reads and processes a CDF file spec ... nOptions:\nResolution - "<>DAMPStrResolution<>" (default: 1)"

DAMPImportBDT :: usage = DAMPImportBDT[filename,samplename] reads and processes a binary BDT ... bout the sample name, this has to be specified as a second parameter (samplename)."

DAMPExportBDT :: usage = DAMPExportBDT[filename,msdata] exports data in a MathDAMP format &l ...  m/z values which can be converted to the range representation should be exported."

DAMPAppendToSampleName :: usage = "DAMPAppendToSampleName[msdata4,string] appends strin ... om previous modifiers by two vertical bars with a space in between (default: True)"

DAMPLoadAnnotationTable :: usage = "DAMPLoadAnnotationTable[filename] loads a list of a ... ve to the label (1 - right, 2 - top, 3 - left, 4 - bottom, 1.5 - top right, etc.)."

DAMPGetIntensities :: usage = "DAMPGetIntensities[msdata,mz] returns a list of signal intensities from msdata corresponding to m/z mz."

DAMPGetChromatogram :: usage = "DAMPGetChromatogram[msdata,mz] returns a chromatogram/e ...  (a list of {time,signal intensity} elements) from msdata corresponding to m/z mz."

DAMPCrop :: usage = "DAMPCrop[msdata,options] reduces the msdata dataset to datapoints  ... )\nTimeRange - two element list specifying the cropping time range (default: All)."

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

DAMPDropMZs :: usage = "DAMPDropMZs[msdata,mzs] reduces the msdata datased by eliminating datapoints corresponding to m/z values specified in the mzs list."<br />

DAMPPlotChromatogram :: usage = "DAMPPlotChromatogram[{msdata,msdata,...},mz,options] p ... specified, the SampleName from each msdata is used as a label (default: Automatic)"

DAMPGradient :: usage = "DAMPGradient[pos1,pos2,color1,color2,backgroundgraylevel] retu ... s1, and color2 at pos2, and finally to darkened color2 at the relative position 1."

DAMPGradientPalette :: usage = "DAMPGradientPalette[options] - generates a color palett ... olor gradients, palette entry for value 0 is shared between the two (default: 100)"

DAMPDrawAnnotation :: usage = "DAMPDrawAnnotation[annotationtable,options] draws the an ... ropriately capture the dimensions of peaks on the ListDensityPlot (default: {1,1})"

DAMPDensityPlot :: usage = "DAMPDensityPlot[msdata,options] plots the msdata using the  ... ons must correspond to the number of passed annotation tables (default: Automatic)"

DAMPParallelPlot :: usage = "DAMPParallelPlot[msdatas,options] plots msdatas (a list of ... ly to the DAMPDensityPlot function which is used internally for plotting the data."

DAMPApplyFunctionToSingle :: usage = "DAMPApplyFunctionToSingle[msdata,function,options ...  to keep track of modifications performed on the dataset (default: \"\")"

DAMPBinChromatogram :: usage = "DAMPBinChromatogram[chromatogram,binsize,options] bins  ...  be applied to signal intensities and timepoints in every interval (default: Mean)"

DAMPBinChromatogramFast :: usage = "DAMPBinChromatogramFast[chromatogram,binsize] bins  ... function DAMPBinChromatogram for a more flexible (and slower) way to bin the data."

DAMPRobustPolynomialFit :: usage = "DAMPRobustPolynomialFit[chromatogram,options] fits  ...  the data for polynomial fitting (default: (DAMPBinChromatogramFast[#,0.25]&))"

DAMPSubtractBaselines :: usage = "DAMPSubtractBaselines[msdata,options] subtracts basel ... ep the track of modifications performed on the dataset (default: \"bs\")"

DAMPRemoveNoise :: usage = "DAMPRemoveNoise[msdata,options] removes noise from every ch ... ep the track of modifications performed on the dataset (default: \"nr\")"

DAMPRemoveSpikes :: usage = "DAMPRemoveSpikes[msdata,options] levels to 0 all signal in ... ep the track of modifications performed on the dataset (default: \"sr\")"

DAMPThreshold :: usage = "DAMPThreshold[msdata,threshold,options] levels to 0 all signa ... to keep track of modifications performed on the dataset (default: \"t\")"

DAMPMovingAverageFast :: usage = "DAMPMovingAverageFast[intensities,windowsize] applies ... ed for the calculation of the average at the beginning or at the end for the list."

DAMPSmooth :: usage = "DAMPSmooth[msdata,options] applies a smoothing function to all c ... to keep track of modifications performed on the dataset (default: \"s\")"

DAMPPickChromatogramPeaks :: usage = "DAMPPickChromatogramPeaks[chromatogram,options] p ... c point for the calculation of centroided retention/migration time (default: 0.05)"

DAMPPickPeaks :: usage = "DAMPPickPeaks[msdata,options] picks peaks from all chromatogr ...  is used internally to pick peaks from individual chromatograms/electropherograms."

DAMPPeakListToAnnotationTable :: usage = "DAMPPeakListToAnnotationTable[peaklist,option ... he position of the text label relative to the annotation label mark (default: 1.5)"

DAMPSelectRepresentativePeaks :: usage = "DAMPSelectRepresentativePeaks[peaklist,option ... eRange - select peaks from this retention/migration time range only (default: All)"

DAMPPlotPeakLayout :: usage = "DAMPPlotPeakLayout[peaklists,options] plots the position ... PlotSymbol[Diamond,3,FilledFalse],PlotSymbol[Box,3,FilledFalse]}})"

DAMPDPScore :: usage = "DAMPDPScore[peaklist1,peaklist2,options] calculates the dynamic ... s function.\nOptions:\nGapPenalty - gap penalty (in minutes) for DP (default: 0.5)"

DAMPFitShiftFunction :: usage = "DAMPFitShiftFunction[peaklist1,peaklist2,options] opti ... n time range of peaks from peaklist1 to be used for scoring (default: {0,∞})"

DAMPAlignPeakList :: usage = "DAMPAlignPeakList[peaklist,timeshiftfunction] applies the ... n the peaklist (expected to have format as returned by the function DAMPPickPeaks)"

DAMPAnnotationTableToPeakList :: usage = "DAMPAnnotationTableToPeakList[annotationtable ... ich resolution the m/z values in the annotation table will be rounded (default: 1)"

DAMPAlignAnnotationTable :: usage = "DAMPAlignAnnotationTable[peaklist,annotationtable, ... .1 m/z resolution, the resolution option should be set to 0.1 as well (default: 1)"

DAMPAlign :: usage = "DAMPAlign[msdata,shiftfunction,timepoints,options] aligns msdata  ... to keep track of modifications performed on the dataset (default: \"a\")"

DAMPNormalize :: usage = "DAMPNormalize[msdata,coefficient,options] multiplies the sign ... eep the track of modifications performed on the dataset (default: \"n\")"

DAMPIntegrate :: usage = "DAMPIntegrate[chromatogram,options] calculates the area below ... ange (default: None). If set to None, baseline is set to signal intensity value 0."

DAMPFilter :: usage = "DAMPFilter[msdata,criteriamsdata,threshold,options] sets to 0 th ... eep the track of modifications performed on the dataset (default: \"f\")"

DAMPTrendFilter :: usage = "DAMPTrendFilter[group1msdatas,group2msdatas,tofiltermsdata, ... ep the track of modifications performed on the dataset (default: \"tf\")"

DAMPApplyFunctionToGroup :: usage = "DAMPApplyFunctionToGroup[msdatas,function,options] ...  the track of the modifications performed on the dataset (default: \"\")"

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

DAMPGenColors :: usage = "DAMPGenColors[number] generates a list of color specification ...  hue range is split proportionally and the colors are assigned from this sequence."

DAMPNormalizeGroup :: usage = "DAMPNormalizeGroup[msdatas,options] aligns msdatas (a li ... ities are rounded to integers in internal calculations and results (default: True)"

DAMPTwoDatasets :: usage = "DAMPTwoDatasets[msdata1,msdata2,options] generates datasets ...  from msdata1 and msdata2 are equal to or greater than this threshold (default: 0)"

DAMPOutliers :: usage = "DAMPOutliers[msdatas,options] highlights the presence of outly ... ed for every dataset in msdatas in addition to the overall result (default: False)"

DAMPTwoGroups :: usage = "DAMPTwoGroups[msdatas1,msdatas2,options] generates datasets r ...  to filter out results originating from individual spikes or outliers (default: 2)"

DAMPMultiGroups :: usage = "DAMPMultiGroups[msdatas,replicates,options] performs the co ...  the SampleName of the first dataset from every group is used (default: Automatic)"

DAMPPlotCandidates :: usage = "DAMPPlotCandidates[msdatas,criteriamsdata,options] plots ... which is used internally to plot the chromatograms/electropherograms (default: {})"