MaConDa                 mass spectrometry contaminants database for PMD
                        check
getcda                  Perform correlation directed analysis for peaks
                        list.
getchain                Get reaction chain for specific mass to charge
                        ratio
getcluster              Get Pseudo-Spectrum as peaks cluster based on
                        pmd analysis.
getcorcluster           Get Pseudo-Spectrum as peaks cluster based on
                        correlation analysis.
getms2pmd               read in MSP file as list for ms/ms annotation
getmspmd                read in MSP file as list for EI-MS annotation
getpaired               Filter ions/peaks based on retention time
                        hierarchical clustering, paired mass
                        distances(PMD) and PMD frequency analysis.
getpmd                  Get pmd for specific reaction
getpmddf                Get pmd details for specific reaction after the
                        removal of isotopouge.
getposneg               Link pos mode peak list with neg mode peak list
                        by pmd.
getrda                  Perform structure/reaction directed analysis
                        for mass only.
getreact                Get quantitative paired peaks list for specific
                        reaction/pmd
getsda                  Perform structure/reaction directed analysis
                        for peaks list.
getstd                  Find the independent ions for each retention
                        time hierarchical clustering based on PMD
                        relationship within each retention time cluster
                        and isotope and return the index of the std
                        data for each retention time cluster.
gettarget               Get multiple injections index for selected
                        retention time
globalstd               GlobalStd algorithm with structure/reaction
                        directed analysis
hmdb                    A dataframe containing HMDB with unique
                        accurate mass pmd with three digits frequency
                        larger than 1 and accuracy percentage larger
                        than 0.9.
keggrall                A dataframe containing reaction related
                        accurate mass pmd and related reaction formula
                        with KEGG ID
omics                   A dataframe containing multiple reaction
                        database ID and their related accurate mass pmd
                        and related reactions
pcasf                   Compare matrices using PCA similarity factor
plotcn                  plot PMD KEGG network for certain compounds and
                        output network average distance and degree
plotpaired              Plot the mass pairs and high frequency mass
                        distances
plotrtg                 Plot the retention time group
plotsda                 Plot the specific structure directed
                        analysis(SDA) groups
plotstd                 Plot the std mass from GlobalStd algorithm
plotstdrt               Plot the std mass from GlobalStd algorithm in
                        certain retention time groups
plotstdsda              Plot the std mass from GlobalStd algorithm in
                        structure directed analysis(SDA) groups
runPMD                  Shiny application for PMD analysis
runPMDnet               Shiny application for PMD network analysis
sda                     A dataset containing common Paired mass
                        distances of substructure, ions replacements,
                        and reaction
spmeinvivo              A peaks list dataset containing 9 samples from
                        3 fish with triplicates samples for each fish
                        from LC-MS.
