addAMDISPeaks           Add AMDIS peak detection results
addChromaTOFPeaks       Add ChromaTOF peak detection results
addXCMSPeaks            addXCMSPeaks
betweenAlignment        Data Structure for "between" alignment of many
                        GCMS samples
calcTimeDiffs           Calculate retention time shifts from profile
                        alignments
clusterAlignment        Data Structure for a collection of all pairwise
                        alignments of GCMS runs
corPrt                  Retention Time Penalized Correlation
de_Duper                deDuper
distToLib               distToLib
dp                      Dynamic programming algorithm, given a
                        similarity matrix
dynRT                   dynRT
eitherMatrix-class      A class description
exportSpectra           exportSpectra
gatherInfo              Gathers abundance informations from an
                        alignment
headToTailPlot          Head to tail plot
importSpec              importSpec
imputePeaks             Imputatin of locations of peaks that were
                        undetected
matchSpec               matchSpec
multipleAlignment-class
                        Data Structure for multiple alignment of many
                        GCMS samples
ndpRT                   Retention Time Penalized Normalized Dot Product
normDotProduct          Normalized Dot Product
parseChromaTOF          Parser for ChromaTOF files
parseELU                Parser for ELU files
peaksAlignment-class    Data Structure for pairwise alignment of 2 GCMS
                        samples
peaksDataset            Data Structure for raw GCMS data and peak
                        detection results
plotAlignedFrags        plotAlignedFrags
plotAlignment,peaksAlignment-method
                        plotAlignment
plotChrom,peaksDataset-method
                        Plotting functions for GCMS data objects
plotClustAlignment,clusterAlignment-method
                        plotClustAlignment
plotFrags               plotFrags
plotImage               Plot of images of GCMS data
progressiveAlignment-class
                        Data Structure for progressive alignment of
                        many GCMS samples
retFatMatrix            retFatMatrix
rmaFitUnit              Fits a robust linear model (RLM) for one
                        metabolite
show,multipleAlignment-method
                        Store the raw data and optionally, information
                        regarding signal peaks for a number of GCMS
                        runs
