Entry: SSgauss
Aliases: SSgauss
Keywords: nonlinear
Description: Gaussian Model
URL: ../../../library/xcms/html/SSgauss.html

Entry: c-methods
Aliases: c.xcmsSet c, c-methods
Keywords: manip
Description: Combine xcmsSet objects
URL: ../../../library/xcms/html/c.xcmsSet.html

Entry: colMax
Aliases: colMax rowMax which.colMax which.rowMax
Keywords: array manip internal
Description: Find row and column maximum values
URL: ../../../library/xcms/html/colMax.html

Entry: descendZero
Aliases: descendZero descendMin descendValue
Keywords: iteration internal
Description: Find start and end points of a peak
URL: ../../../library/xcms/html/descendZero.html

Entry: diffreport-methods
Aliases: diffreport diffreport,xcmsSet-method
Keywords: methods file
Description: Create report of analyte differences
URL: ../../../library/xcms/html/diffreport-methods.html

Entry: doubleMatrix
Aliases: doubleMatrix integerMatrix logicalMatrix
Keywords: programming internal
Description: Allocate double, integer, or logical matricies
URL: ../../../library/xcms/html/doubleMatrix.html

Entry: etg
Aliases: etg
Keywords: models
Description: Empirically Transformed Gaussian function
URL: ../../../library/xcms/html/etg.html

Entry: fillPeaks-methods
Aliases: fillPeaks fillPeaks,xcmsSet-method
Keywords: methods file
Description: Integrate areas of missing peaks
URL: ../../../library/xcms/html/fillPeaks-methods.html

Entry: filtfft
Aliases: filtfft
Keywords: math internal
Description: Apply an convolution filter using an FFT
URL: ../../../library/xcms/html/filtfft.html

Entry: findEqualGreater
Aliases: findEqualGreater findEqualLess findEqualGreaterM findRange
Keywords: utilities internal
Description: Find values in sorted vectors
URL: ../../../library/xcms/html/findEqualGreater.html

Entry: findPeaks-methods
Aliases: findPeaks-methods findPeaks findPeaks,xcmsRaw-method
Keywords: methods
Description: Feature detection for GC/MS and LC/MS Data - methods
URL: ../../../library/xcms/html/findPeaks-methods.html

Entry: findPeaks.MSW-methods
Aliases: findPeaks.MSW findPeaks.MSW,xcmsRaw-method
Keywords: methods
Description: Feature detection for single-spectrum non-chromatography MS data
URL: ../../../library/xcms/html/findPeaks.MSW-methods.html

Entry: findPeaks.centWave-methods
Aliases: findPeaks.centWave findPeaks.centWave,xcmsRaw-method
Keywords: methods
Description: Feature detection for high resolution LC/MS data
URL: ../../../library/xcms/html/findPeaks.centWave-methods.html

Entry: findPeaks.matchedFilter-methods
Aliases: findPeaks.matchedFilter findPeaks.matchedFilter,xcmsRaw-method
Keywords: methods
Description: Feature detection in the chromatographic time domain
URL: ../../../library/xcms/html/findPeaks.matchedFilter-methods.html

Entry: getEIC-methods
Aliases: getEIC getEIC,xcmsRaw-method getEIC,xcmsSet-method
Keywords: methods file
Description: Get extracted ion chromatograms for specified m/z ranges
URL: ../../../library/xcms/html/getEIC-methods.html

Entry: getPeaks-methods
Aliases: getPeaks getPeaks,xcmsRaw-method
Keywords: methods manip
Description: Get peak intensities for specified regions
URL: ../../../library/xcms/html/getPeaks-methods.html

Entry: getScan-methods
Aliases: getScan getScan,xcmsRaw-method
Keywords: methods manip
Description: Get m/z and intensity values for a single mass scan
URL: ../../../library/xcms/html/getScan-methods.html

Entry: getSpec-methods
Aliases: getSpec getSpec,xcmsRaw-method
Keywords: methods manip
Description: Get average m/z and intensity values for multiple mass scans
URL: ../../../library/xcms/html/getSpec-methods.html

Entry: group-methods
Aliases: group group,xcmsSet-method
Keywords: methods file
Description: Group peaks from different samples together
URL: ../../../library/xcms/html/group-methods.html

Entry: groupnames-methods
Aliases: groupnames groupnames,xcmsEIC-method groupnames,xcmsSet-method
Keywords: methods file
Description: Generate unque names for peak groups
URL: ../../../library/xcms/html/groupnames-methods.html

Entry: groupval-methods
Aliases: groupval groupval,xcmsSet-method
Keywords: methods manip
Description: Extract a matrix of peak values for each group
URL: ../../../library/xcms/html/groupval-methods.html

Entry: image-methods
Aliases: image.xcmsRaw image, image-methods
Keywords: hplot
Description: Plot log intensity image of a xcmsRaw object
URL: ../../../library/xcms/html/image.xcmsRaw.html

Entry: medianFilter
Aliases: medianFilter
Keywords: manip
Description: Apply a median filter to a matrix
URL: ../../../library/xcms/html/medianFilter.html

Entry: na.flatfill
Aliases: na.flatfill
Keywords: NA internal
Description: Fill in NA values at the extremes of a vector
URL: ../../../library/xcms/html/na.flatfill.html

Entry: netCDF
Aliases: netCDFStrError netCDFIsFile netCDFOpen netCDFClose netCDFVarID netCDFVarLen netCDFVarDouble netCDFVarInt netCDFMSPoints netCDFRawData
Keywords: file internal
Description: High-performance, low-level access to NetCDF data files
URL: ../../../library/xcms/html/netCDF.html

Entry: panel.cor
Aliases: panel.cor
Keywords: aplot internal
Description: Correlation coefficient panel for pairs function
URL: ../../../library/xcms/html/panel.cor.html

Entry: plot.xcmsEIC
Aliases: plot.xcmsEIC plot, plot-methods
Keywords: methods hplot
Description: Plot extracted ion chromatograms from multiple files
URL: ../../../library/xcms/html/plot.xcmsEIC.html

Entry: plotChrom-methods
Aliases: plotChrom plotChrom,xcmsRaw-method
Keywords: methods hplot iplot
Description: Plot extracted ion chromatograms from the profile matrix
URL: ../../../library/xcms/html/plotChrom-methods.html

Entry: plotPeaks-methods
Aliases: plotPeaks plotPeaks,xcmsRaw-method
Keywords: methods hplot
Description: Plot a grid of a large number of peaks
URL: ../../../library/xcms/html/plotPeaks-methods.html

Entry: plotRaw-methods
Aliases: plotRaw plotRaw,xcmsRaw-method
Keywords: methods hplot
Description: Scatterplot of raw data points
URL: ../../../library/xcms/html/plotRaw-methods.html

Entry: plotScan-methods
Aliases: plotScan plotScan,xcmsRaw-method
Keywords: methods hplot
Description: Plot a single mass scan
URL: ../../../library/xcms/html/plotScan-methods.html

Entry: plotSpec-methods
Aliases: plotSpec plotSpec,xcmsRaw-method
Keywords: methods hplot iplot
Description: Plot mass spectra from the profile matrix
URL: ../../../library/xcms/html/plotSpec-methods.html

Entry: plotSurf-methods
Aliases: plotSurf plotSurf,xcmsRaw-method
Keywords: methods hplot iplot
Description: Plot profile matrix 3D surface using OpenGL
URL: ../../../library/xcms/html/plotSurf-methods.html

Entry: plotTIC-methods
Aliases: plotTIC plotTIC,xcmsRaw-method
Keywords: methods hplot iplot
Description: Plot total ion count
URL: ../../../library/xcms/html/plotTIC-methods.html

Entry: plotrt-methods
Aliases: plotrt plotrt,xcmsSet-method
Keywords: methods hplot
Description: Plot retention time deviation profiles
URL: ../../../library/xcms/html/plotrt-methods.html

Entry: profGenerate
Aliases: profBin profBinM profBinLin profBinLinM profBinLinBase profBinLinBaseM profIntLin profIntLinM profMaxIdx profMaxIdxM
Keywords: manip internal
Description: Generation of profile data
URL: ../../../library/xcms/html/profGenerate.html

Entry: profMedFilt-methods
Aliases: profMedFilt profMedFilt,xcmsRaw-method
Keywords: methods manip
Description: Median filtering of the profile matrix
URL: ../../../library/xcms/html/profMedFilt-methods.html

Entry: profMethod-methods
Aliases: profMethod profMethod<- profMethod,xcmsRaw-method profMethod<-,xcmsRaw-method
Keywords: methods manip
Description: Get and set method for generating profile data
URL: ../../../library/xcms/html/profMethod-methods.html

Entry: profRange-methods
Aliases: profRange profRange,xcmsRaw-method
Keywords: methods manip
Description: Specify a subset of profile mode data
URL: ../../../library/xcms/html/profRange-methods.html

Entry: profStep-methods
Aliases: profStep profStep<- profStep,xcmsRaw-method profStep<-,xcmsRaw-method
Keywords: methods manip
Description: Get and set m/z step for generating profile data
URL: ../../../library/xcms/html/profStep-methods.html

Entry: pval
Aliases: pval
Keywords: univar internal
Description: Generate p-values for a vector of t-statistics
URL: ../../../library/xcms/html/pval.html

Entry: ramp
Aliases: rampInit rampPrintFiles rampIsFile rampOpen rampClose rampCloseAll rampNumScans rampScanHeaders rampSIPeaks rampRawData
Keywords: file internal
Description: High-performance, low-level access to mzXML/mzData files
URL: ../../../library/xcms/html/ramp.html

Entry: rawEIC-methods
Aliases: rawEIC rawEIC,xcmsRaw-method
Keywords: methods
Description: Get extracted ion chromatograms for specified m/z range
URL: ../../../library/xcms/html/rawEIC-methods.html

Entry: rectUnique
Aliases: rectUnique
Keywords: array internal
Description: Determine a subset of rectangles with unique, non-overlapping areas
URL: ../../../library/xcms/html/rectUnique.html

Entry: retcor-methods
Aliases: retcor retcor,xcmsSet-method
Keywords: methods file
Description: Align retention times across samples
URL: ../../../library/xcms/html/retcor-methods.html

Entry: retexp
Aliases: retexp
Keywords: manip
Description: Set retention time window to a specified width
URL: ../../../library/xcms/html/retexp.html

Entry: sampnames-methods
Aliases: sampnames sampnames,xcmsEIC-method sampnames,xcmsSet-method
Keywords: methods file
Description: Get sample names
URL: ../../../library/xcms/html/sampnames-methods.html

Entry: specNoise
Aliases: specNoise
Keywords: manip
Description: Calculate noise for a sparse continuum mass spectrum
URL: ../../../library/xcms/html/specNoise.html

Entry: specPeaks
Aliases: specPeaks
Keywords: manip
Description: Identify peaks in a sparse continuum mode spectrum
URL: ../../../library/xcms/html/specPeaks.html

Entry: split.xcmsSet
Aliases: split.xcmsSet split, split-methods
Keywords: manip
Description: Divide an xcmsSet object
URL: ../../../library/xcms/html/split.xcmsSet.html

Entry: xcmsEIC-class
Aliases: xcmsEIC-class mzrange,xcmsEIC-method mzrange rtrange,xcmsEIC-method rtrange show,xcmsEIC-method
Keywords: classes
Description: Class xcmsEIC, a class for multi-sample extracted ion chromatograms
URL: ../../../library/xcms/html/xcmsEIC-class.html

Entry: xcmsRaw-class
Aliases: xcmsRaw-class profMz,xcmsRaw-method profMz revMz,xcmsRaw-method revMz show,xcmsRaw-method sortMz,xcmsRaw-method sortMz
Keywords: classes
Description: Class xcmsRaw, a class for handling raw data
URL: ../../../library/xcms/html/xcmsRaw-class.html

Entry: xcmsRaw
Aliases: xcmsRaw
Keywords: file
Description: Constructor for xcmsRaw objects which reads NetCDF/mzXML files
URL: ../../../library/xcms/html/xcmsRaw.html

Entry: xcmsSet-class
Aliases: xcmsSet-class cdfpaths<-,xcmsSet-method cdfpaths<- cdfpaths,xcmsSet-method cdfpaths groupidx<-,xcmsSet-method groupidx<- groupidx,xcmsSet-method groupidx groups<-,xcmsSet-method groups<- groups,xcmsSet-method groups peaks<-,xcmsSet-method peaks<- peaks,xcmsSet-method peaks profinfo<-,xcmsSet-method profinfo<- profinfo,xcmsSet-method profinfo sampclass<-,xcmsSet-method sampclass<- sampclass,xcmsSet-method sampclass sampnames<-,xcmsSet-method sampnames<- show,xcmsSet-method
Keywords: classes
Description: Class xcmsSet, a class for preprocessing peak data
URL: ../../../library/xcms/html/xcmsSet-class.html

Entry: xcmsSet
Aliases: xcmsSet
Keywords: file
Description: Constructor for xcmsSet objects which finds peaks in NetCDF/mzXML files
URL: ../../../library/xcms/html/xcmsSet.html
