mzmatch.R: mzmatch and PeakML integration for XCMS.

This package provides integration between the PeakML Java library (and its file formats) and the XCMS library.

AuthorRichard Scheltema <r.a.scheltema@rug.nl>, Andris Jankevics <a.jankevics@rug.nl>, Achuthanuni Chokkathukalam (unni.chokkathukalam@glasgow.ac.uk).
Date of publication2015-02-13 14:36:40
MaintainerAndris Jankevics <andris.jankevics@manchester.ac.uk>
LicenseGPL (>= 2)
Version2.0-13

View on R-Forge

Man pages

mzmatch.init: mzmatch.init

mzmatch.ipeak.align.CowCoda: mzmatch.ipeak.align.CowCoda

mzmatch.ipeak.Combine: mzmatch.ipeak.Combine

mzmatch.ipeak.convert.ConvertToText: mzmatch.ipeak.convert.ConvertToText

mzmatch.ipeak.db.CreateCycDB: mzmatch.ipeak.db.CreateCycDB

mzmatch.ipeak.db.CreateHMDB: mzmatch.ipeak.db.CreateHMDB

mzmatch.ipeak.db.CreateLMDB: mzmatch.ipeak.db.CreateLMDB

mzmatch.ipeak.db.DBToText: mzmatch.ipeak.db.DBToText

mzmatch.ipeak.ExtractBackgroundIons: mzmatch.ipeak.ExtractBackgroundIons

mzmatch.ipeak.filter.FilterCluster: mzmatch.ipeak.filter.FilterCluster

mzmatch.ipeak.filter.FilterOnRelationIDs: mzmatch.ipeak.filter.FilterOnRelationIDs

mzmatch.ipeak.filter.NoiseFilter: mzmatch.ipeak.filter.NoiseFilter

mzmatch.ipeak.filter.RSDFilter: mzmatch.ipeak.filter.RSDFilter

mzmatch.ipeak.filter.SimpleFilter: mzmatch.ipeak.filter.SimpleFilter

mzmatch.ipeak.graphics.PeakMLToTIC: mzmatch.ipeak.graphics.PeakMLToTIC

mzmatch.ipeak.normalisation.Normalisation: mzmatch.ipeak.normalisation.Normalisation

mzmatch.ipeak.normalisation.VanDeSompele: mzmatch.ipeak.normalisation.VanDeSompele

mzmatch.ipeak.sort.MetAssign: mzmatch.ipeak.sort.MetAssign

mzmatch.ipeak.sort.PeakSort: mzmatch.ipeak.sort.PeakSort

mzmatch.ipeak.sort.RelatedPeaks: mzmatch.ipeak.sort.RelatedPeaks

mzmatch.ipeak.util.BreakupRelated: mzmatch.ipeak.util.BreakupRelated

mzmatch.ipeak.util.ExtractSets: mzmatch.ipeak.util.ExtractSets

mzmatch.ipeak.util.Identify: mzmatch.ipeak.util.Identify

mzmatch.ipeak.util.Recovery: mzmatch.ipeak.util.Recovery

mzmatch.R-package: mzmatch and PeakML integration for XCMS and R

mzmatch.R.Setup: mzmatch.R.Setup

mzmatch.XML.data.base.parser: mzmatch.XML.data.base.parser

PeakML.BlankFilter: PeakML.BlankFilter

PeakML.bubbleplot: PeakML.bubbleplot

PeakML.ComparePeakSets: PeakML.ComparePeakSets

PeakML.DilutionTrendFilter: PeakML.DilutionTrendFilter

PeakML.FilterPeakGroups: PeakML.FilterPeakGroups

PeakML.GapFiller: PeakML.GapFiller

PeakML.get.attributes: PeakML.get.attributes

PeakML.Isotope.DB2Text: PeakML.Isotope.DB2Text

PeakML.Isotope.filteroutUnlabelled: PeakML.Isotope.filteroutUnlabelled

PeakML.Isotope.filterPeaks: PeakML.Isotope.filterPeaks

PeakML.Isotope.getAbunMtxList: PeakML.Isotope.getAbunMtxList

PeakML.Isotope.getChromData: PeakML.Isotope.getChromData

PeakML.Isotope.getFCMtx: PeakML.Isotope.getFCMtx

PeakML.Isotope.getFCMtxAbun: PeakML.Isotope.getFCMtxAbun

PeakML.Isotope.getIsotopes: PeakML.Isotope.getIsotopes

PeakML.Isotope.getMassWindow: PeakML.Isotope.getMassWindow

PeakML.Isotope.getRatioMtxList: PeakML.Isotope.getRatioMtxList

PeakML.Isotope.getTrendList: PeakML.Isotope.getTrendList

PeakML.Isotope.getTrendMtx: PeakML.Isotope.getTrendMtx

PeakML.Isotope.plotSamples: PeakML.Isotope.plotSamples

PeakML.Isotope.plotUntargettedIsotopes: PeakML.Isotope.plotUntargettedIsotopes

PeakML.Isotope.processTargettedIsotopes: PeakML.Isotope.processTargettedIsotopes

PeakML.Isotope.processUntargettedIsotopes: PeakML.Isotope.processUntargettedIsotopes

PeakML.Isotope.ReadDB: PeakML.Isotope.ReadDB

PeakML.Isotope.TargettedIsotopes: PeakML.Isotope.TargettedIsotopes

PeakML.Isotope.UntargettedIsotopes: PeakML.Isotope.UntargettedIsotopes

PeakML.Methods.baseCorrection: PeakML.Methods.baseCorrection

PeakML.Methods.combinePeakMLfiles: PeakML.Methods.combinePeakMLfiles

PeakML.Methods.DBidToCompoundName: PeakML.Methods.DBidToCompoundName

PeakML.Methods.extractFileName: PeakML.Methods.extractFileName

PeakML.Methods.extractPeakSets: PeakML.Methods.extractPeakGroups

PeakML.Methods.formula2mass: PeakML.Methods.formula2mass

PeakML.Methods.getCarbon: PeakML.Methods.getCarbon

PeakML.Methods.getChromData: PeakML.Methods.getChromData

PeakML.Methods.getCompleteTable: PeakML.Methods.getCompleteTable

PeakML.Methods.getElements: PeakML.Methods.getElements

PeakML.Methods.getGroupAnnotations: PeakML.Methods.getGroupAnnotations

PeakML.Methods.getMassCorrection: PeakML.Methods.getMassCorrection

PeakML.Methods.getPeakData: PeakML.Methods.getPeakData

PeakML.Methods.getPhenoData: PeakML.Methods.getPhenoData

PeakML.Methods.getPPMMass: PeakML.Methods.getPPMMass

PeakML.Methods.getPPMWindow: PeakML.Methods.getPPMWindow

PeakML.Methods.getProtonCoef: PeakML.Methods.getProtonCoef

PeakML.Methods.getProtonMass: PeakML.Methods.getProtonMass

PeakML.Methods.getRawDataPaths: PeakML.Methods.getRawDataPaths

PeakML.Methods.getRawMat: PeakML.Methods.getRawMat

PeakML.Methods.getRawSignals: PeakML.Methods.getRawSignals

PeakML.Methods.getRTWindow: PeakML.Methods.getRTWindow

PeakML.Methods.getRTWindowFromString: PeakML.Methods.getRTWindowFromString

PeakML.Methods.getStdErr: PeakML.Methods.getStdErr

PeakML.Methods.PeakShapeCorrelation: PeakML.Methods.PeakShapeCorrelation

PeakML.Methods.writeGroupAnnotations: PeakML.Methods.writeGroupAnnotations

PeakML.Normalization: PeakML.Normalization

PeakML.Plot.BarPlot: PeakML.Plot.BarPlot

PeakML.Plot.Chromatograms: PeakML.Plot.Chromatograms

PeakML.Plot.RankProducts: PeakML.Plot.RankProducts

PeakML.Plot.RelatedPeaks: PeakML.Plot.RelatedPeaks

PeakML.RankProducts: PeakML.RankProducts

PeakML.Read: PeakML.Read

PeakML.trendPlot: PeakML.trendPlot

PeakML.Viewer: PeakML.Viewer

PeakML.Write: PeakML.Write

PeakML.xcms.read: PeakML.xcms.read

PeakML.xcms.write: PeakML.xcms.write

PeakML.xcms.write.SingleInstance: PeakML.xcms.write.SingleInstance

PeakML.xcms.write.SingleMeasurement: PeakML.xcms.write.SingleMeasurement

RCreateXMLDB: RCreateXMLDB

TrendPlot: TrendPlot

Files in this package

mzmatch.R/DESCRIPTION
mzmatch.R/NAMESPACE
mzmatch.R/R
mzmatch.R/R/PeakML.BlankFilter.R mzmatch.R/R/PeakML.ComparePeakSets.R mzmatch.R/R/PeakML.DilutionTrendFilter.R mzmatch.R/R/PeakML.FilterPeakGroups.R mzmatch.R/R/PeakML.GapFiller.R mzmatch.R/R/PeakML.Isotope.DB2Text.R mzmatch.R/R/PeakML.Isotope.ReadDB.R mzmatch.R/R/PeakML.Isotope.TargettedIsotopes.R mzmatch.R/R/PeakML.Isotope.UntargettedIsotopes.R mzmatch.R/R/PeakML.Isotope.filterPeaks.R mzmatch.R/R/PeakML.Isotope.filteroutUnlabelled.R mzmatch.R/R/PeakML.Isotope.getAbunMtxList.R mzmatch.R/R/PeakML.Isotope.getChromData.R mzmatch.R/R/PeakML.Isotope.getFCMtx.R mzmatch.R/R/PeakML.Isotope.getFCMtxAbun.R mzmatch.R/R/PeakML.Isotope.getIsotopes.R mzmatch.R/R/PeakML.Isotope.getMassWindow.R mzmatch.R/R/PeakML.Isotope.getRatioMtxList.R mzmatch.R/R/PeakML.Isotope.getTrendList.R mzmatch.R/R/PeakML.Isotope.getTrendMtx.R mzmatch.R/R/PeakML.Isotope.plotSamples.R mzmatch.R/R/PeakML.Isotope.plotUntargettedIsotopes.R mzmatch.R/R/PeakML.Isotope.processTargettedIsotopes.R mzmatch.R/R/PeakML.Isotope.processUntargettedIsotopes.R mzmatch.R/R/PeakML.Methods.DBidToCompoundName.R mzmatch.R/R/PeakML.Methods.PeakShapeCorrelation.R mzmatch.R/R/PeakML.Methods.baseCorrection.R mzmatch.R/R/PeakML.Methods.combinePeakMLfiles.R mzmatch.R/R/PeakML.Methods.extractFileName.R mzmatch.R/R/PeakML.Methods.extractPeakGroups.R mzmatch.R/R/PeakML.Methods.formula2mass.R mzmatch.R/R/PeakML.Methods.getCarbon.R mzmatch.R/R/PeakML.Methods.getChromData.R mzmatch.R/R/PeakML.Methods.getCompleteTable.R mzmatch.R/R/PeakML.Methods.getESIpolarity.R mzmatch.R/R/PeakML.Methods.getElements.R mzmatch.R/R/PeakML.Methods.getGroupAnnotations.R mzmatch.R/R/PeakML.Methods.getMassCorrection.R mzmatch.R/R/PeakML.Methods.getPPMMass.R mzmatch.R/R/PeakML.Methods.getPPMWindow.R mzmatch.R/R/PeakML.Methods.getPeakData.R mzmatch.R/R/PeakML.Methods.getPhenoData.R mzmatch.R/R/PeakML.Methods.getProtonCoef.R mzmatch.R/R/PeakML.Methods.getProtonMass.R mzmatch.R/R/PeakML.Methods.getRTWindow.R mzmatch.R/R/PeakML.Methods.getRTWindowFromString.R mzmatch.R/R/PeakML.Methods.getRawDataPaths.R mzmatch.R/R/PeakML.Methods.getRawMat.R mzmatch.R/R/PeakML.Methods.getRawSignals.R mzmatch.R/R/PeakML.Methods.getStdErr.R mzmatch.R/R/PeakML.Methods.mzML.startTimeStamp.R mzmatch.R/R/PeakML.Methods.writeGroupAnnotations.R mzmatch.R/R/PeakML.Normalization.R mzmatch.R/R/PeakML.PeakChopper.R mzmatch.R/R/PeakML.Plot.BarPlot.R mzmatch.R/R/PeakML.Plot.Chromatograms.R mzmatch.R/R/PeakML.Plot.RankProducts.R mzmatch.R/R/PeakML.Plot.RelatedPeaks.R mzmatch.R/R/PeakML.QCIntensityCorrection.R mzmatch.R/R/PeakML.QCRSDFilter.R mzmatch.R/R/PeakML.QCSignalCorrection.R mzmatch.R/R/PeakML.RankProducts.R mzmatch.R/R/PeakML.Read.R mzmatch.R/R/PeakML.Viewer.R mzmatch.R/R/PeakML.Write.R mzmatch.R/R/PeakML.bubbleplot.R mzmatch.R/R/PeakML.get.attributes.R mzmatch.R/R/PeakML.trendPlot.R mzmatch.R/R/PeakML.xcms.read.R mzmatch.R/R/PeakML.xcms.write.R mzmatch.R/R/PeakML.xcms.write.SingleInstance.R mzmatch.R/R/PeakML.xcms.write.SingleMeasurement.R mzmatch.R/R/RCreateXMLDB.R mzmatch.R/R/TrendPlot.R mzmatch.R/R/mzmatch.R.Setup.R mzmatch.R/R/mzmatch.XML.data.base.parser.R mzmatch.R/R/mzmatch.init.R mzmatch.R/R/mzmatch.ipeak.Combine.R mzmatch.R/R/mzmatch.ipeak.ExtractBackgroundIons.R mzmatch.R/R/mzmatch.ipeak.align.CowCoda.R mzmatch.R/R/mzmatch.ipeak.convert.ConvertToText.R mzmatch.R/R/mzmatch.ipeak.db.CreateCycDB.R mzmatch.R/R/mzmatch.ipeak.db.CreateHMDB.R mzmatch.R/R/mzmatch.ipeak.db.CreateLMDB.R mzmatch.R/R/mzmatch.ipeak.db.DBToText.R mzmatch.R/R/mzmatch.ipeak.filter.FilterCluster.R mzmatch.R/R/mzmatch.ipeak.filter.FilterOnRelationIDs.R mzmatch.R/R/mzmatch.ipeak.filter.NoiseFilter.R mzmatch.R/R/mzmatch.ipeak.filter.RSDFilter.R mzmatch.R/R/mzmatch.ipeak.filter.SimpleFilter.R mzmatch.R/R/mzmatch.ipeak.graphics.PeakMLToTIC.R mzmatch.R/R/mzmatch.ipeak.normalisation.Normalisation.R mzmatch.R/R/mzmatch.ipeak.normalisation.VanDeSompele.R mzmatch.R/R/mzmatch.ipeak.sort.MetAssign.R mzmatch.R/R/mzmatch.ipeak.sort.PeakSort.R mzmatch.R/R/mzmatch.ipeak.sort.RelatedPeaks.R mzmatch.R/R/mzmatch.ipeak.util.BreakupRelated.R mzmatch.R/R/mzmatch.ipeak.util.ExtractSets.R mzmatch.R/R/mzmatch.ipeak.util.Identify.R mzmatch.R/R/mzmatch.ipeak.util.Recovery.R
mzmatch.R/man
mzmatch.R/man/PeakML.BlankFilter.Rd mzmatch.R/man/PeakML.ComparePeakSets.Rd mzmatch.R/man/PeakML.DilutionTrendFilter.Rd mzmatch.R/man/PeakML.FilterPeakGroups.Rd mzmatch.R/man/PeakML.GapFiller.Rd mzmatch.R/man/PeakML.Isotope.DB2Text.Rd mzmatch.R/man/PeakML.Isotope.ReadDB.Rd mzmatch.R/man/PeakML.Isotope.TargettedIsotopes.Rd mzmatch.R/man/PeakML.Isotope.UntargettedIsotopes.Rd mzmatch.R/man/PeakML.Isotope.filterPeaks.Rd mzmatch.R/man/PeakML.Isotope.filteroutUnlabelled.Rd mzmatch.R/man/PeakML.Isotope.getAbunMtxList.Rd mzmatch.R/man/PeakML.Isotope.getChromData.Rd mzmatch.R/man/PeakML.Isotope.getFCMtx.Rd mzmatch.R/man/PeakML.Isotope.getFCMtxAbun.Rd mzmatch.R/man/PeakML.Isotope.getIsotopes.Rd mzmatch.R/man/PeakML.Isotope.getMassWindow.Rd mzmatch.R/man/PeakML.Isotope.getRatioMtxList.Rd mzmatch.R/man/PeakML.Isotope.getTrendList.Rd mzmatch.R/man/PeakML.Isotope.getTrendMtx.Rd mzmatch.R/man/PeakML.Isotope.plotSamples.Rd mzmatch.R/man/PeakML.Isotope.plotUntargettedIsotopes.Rd mzmatch.R/man/PeakML.Isotope.processTargettedIsotopes.Rd mzmatch.R/man/PeakML.Isotope.processUntargettedIsotopes.Rd mzmatch.R/man/PeakML.Methods.DBidToCompoundName.Rd mzmatch.R/man/PeakML.Methods.PeakShapeCorrelation.Rd mzmatch.R/man/PeakML.Methods.baseCorrection.Rd mzmatch.R/man/PeakML.Methods.combinePeakMLfiles.Rd mzmatch.R/man/PeakML.Methods.extractFileName.Rd mzmatch.R/man/PeakML.Methods.extractPeakSets.Rd mzmatch.R/man/PeakML.Methods.formula2mass.Rd mzmatch.R/man/PeakML.Methods.getCarbon.Rd mzmatch.R/man/PeakML.Methods.getChromData.Rd mzmatch.R/man/PeakML.Methods.getCompleteTable.Rd mzmatch.R/man/PeakML.Methods.getElements.Rd mzmatch.R/man/PeakML.Methods.getGroupAnnotations.Rd mzmatch.R/man/PeakML.Methods.getMassCorrection.Rd mzmatch.R/man/PeakML.Methods.getPPMMass.Rd mzmatch.R/man/PeakML.Methods.getPPMWindow.Rd mzmatch.R/man/PeakML.Methods.getPeakData.Rd mzmatch.R/man/PeakML.Methods.getPhenoData.Rd mzmatch.R/man/PeakML.Methods.getProtonCoef.Rd mzmatch.R/man/PeakML.Methods.getProtonMass.Rd mzmatch.R/man/PeakML.Methods.getRTWindow.Rd mzmatch.R/man/PeakML.Methods.getRTWindowFromString.Rd mzmatch.R/man/PeakML.Methods.getRawDataPaths.Rd mzmatch.R/man/PeakML.Methods.getRawMat.Rd mzmatch.R/man/PeakML.Methods.getRawSignals.Rd mzmatch.R/man/PeakML.Methods.getStdErr.Rd mzmatch.R/man/PeakML.Methods.writeGroupAnnotations.Rd mzmatch.R/man/PeakML.Normalization.Rd mzmatch.R/man/PeakML.Plot.BarPlot.Rd mzmatch.R/man/PeakML.Plot.Chromatograms.Rd mzmatch.R/man/PeakML.Plot.RankProducts.Rd mzmatch.R/man/PeakML.Plot.RelatedPeaks.Rd mzmatch.R/man/PeakML.RankProducts.Rd mzmatch.R/man/PeakML.Read.Rd mzmatch.R/man/PeakML.Viewer.Rd mzmatch.R/man/PeakML.Write.Rd mzmatch.R/man/PeakML.bubbleplot.Rd mzmatch.R/man/PeakML.get.attributes.Rd mzmatch.R/man/PeakML.trendPlot.Rd mzmatch.R/man/PeakML.xcms.read.Rd mzmatch.R/man/PeakML.xcms.write.Rd mzmatch.R/man/PeakML.xcms.write.SingleInstance.Rd mzmatch.R/man/PeakML.xcms.write.SingleMeasurement.Rd mzmatch.R/man/RCreateXMLDB.Rd mzmatch.R/man/TrendPlot.Rd mzmatch.R/man/mzmatch.R-package.Rd mzmatch.R/man/mzmatch.R.Setup.Rd mzmatch.R/man/mzmatch.XML.data.base.parser.Rd mzmatch.R/man/mzmatch.init.Rd mzmatch.R/man/mzmatch.ipeak.Combine.Rd mzmatch.R/man/mzmatch.ipeak.ExtractBackgroundIons.Rd mzmatch.R/man/mzmatch.ipeak.align.CowCoda.Rd mzmatch.R/man/mzmatch.ipeak.convert.ConvertToText.Rd mzmatch.R/man/mzmatch.ipeak.db.CreateCycDB.Rd mzmatch.R/man/mzmatch.ipeak.db.CreateHMDB.Rd mzmatch.R/man/mzmatch.ipeak.db.CreateLMDB.Rd mzmatch.R/man/mzmatch.ipeak.db.DBToText.Rd mzmatch.R/man/mzmatch.ipeak.filter.FilterCluster.Rd mzmatch.R/man/mzmatch.ipeak.filter.FilterOnRelationIDs.Rd mzmatch.R/man/mzmatch.ipeak.filter.NoiseFilter.Rd mzmatch.R/man/mzmatch.ipeak.filter.RSDFilter.Rd mzmatch.R/man/mzmatch.ipeak.filter.SimpleFilter.Rd mzmatch.R/man/mzmatch.ipeak.graphics.PeakMLToTIC.Rd mzmatch.R/man/mzmatch.ipeak.normalisation.Normalisation.Rd mzmatch.R/man/mzmatch.ipeak.normalisation.VanDeSompele.Rd mzmatch.R/man/mzmatch.ipeak.sort.MetAssign.Rd mzmatch.R/man/mzmatch.ipeak.sort.PeakSort.Rd mzmatch.R/man/mzmatch.ipeak.sort.RelatedPeaks.Rd mzmatch.R/man/mzmatch.ipeak.util.BreakupRelated.Rd mzmatch.R/man/mzmatch.ipeak.util.ExtractSets.Rd mzmatch.R/man/mzmatch.ipeak.util.Identify.Rd mzmatch.R/man/mzmatch.ipeak.util.Recovery.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.