GetIntegration          GetIntegration was mainly used for get the
                        integration of certain ion's chromatogram data
                        and plot the data
Getisotopologues        Get the selected isotopologues at certain MS
                        data
Integration             Just integrate data according to fixed rt and
                        fixed noise area
Mode                    define the Mode function
TBBPA                   Demo data for TBBPA metabolism in Pumpkin
batch                   Get the MIR and related information from the
                        files
cbmd                    Combine two data with similar retention time
                        while different mass range
dotpanno                Perform MS/MS dot product annotation for mgf
                        file
findline                find line of the regression model for GC-MS
findlipid               Find lipid class of metabolites base on
                        referenced Kendrick mass defect
findmet                 Screen metabolites by Mass Defect
findohc                 Screen organohalogen compounds by retention
                        time, mass defect analysis and isotope
                        relationship modified by literature report.
                        Also support compounds with [M] and [M+2] ratio
                        cutoff.
findpfc                 Find PFCs based on mass defect analysis
getMSP                  read in MSP file as list for ms/ms or ms(EI)
                        annotation
getQCraw                get the data of QC compound for a group of data
getalign                Align two peaks vectors by mass to charge ratio
                        and/or retention time
getalign2               Align mass to charge ratio and/or retention
                        time to remove redundancy
getbgremove             Get the peak list with blank samples' peaks
                        removed
getbiotechrep           Get the report for biological replicates.
getcompare              Align multiple peaks list to one peak list
getcsv                  Convert an list object to csv file.
getdata                 Get xcmsset object in one step with optimized
                        methods.
getdata2                Get XCMSnExp object in one step from structured
                        folder path for xcms 3.
getdoe                  Generate the group level rsd and average
                        intensity based on DoE,
getdwtus                Density weighted intensity for one sample
getfeaturesanova        Get the features from anova, with p value, q
                        value, rsd and power restriction
getfeaturest            Get the features from t test, with p value, q
                        value, rsd and power restriction
getfilter               Filter the data based on row and column index
getformula              Get chemical formula for mass to charge ratio.
getgrouprep             Get the report for samples with biological and
                        technique replicates in different groups
getimputation           Impute the peaks list data
getmass                 Get the exact mass of the isotopologues from a
                        chemical formula or reaction's isotope patterns
                        with the highest abundances
getmassdefect           Get mass defect with certain scaled factor
getmd                   Import data and return the annotated matrix for
                        GC/LC-MS by m/z range and retention time
getmdh                  Get the high order unit based Mass Defect
getmdr                  Get the raw Mass Defect
getmr                   Get the mzrt profile and group information for
                        batch correction and plot as a list directly
                        from path with default setting
getms1anno              Annotation of MS1 data by compounds database by
                        predefined paired mass distance
getmzrt                 Get the mzrt profile and group information as a
                        mzrt list and/or save them as csv or rds for
                        further analysis.
getmzrt2                Get the mzrt profile and group information for
                        batch correction and plot as a list for xcms 3
                        object
getmzrtcsv              Covert the peaks list csv file into list
getoverlappeak          Get the overlap peaks by mass and retention
                        time range
getpn                   Merge positive and negative mode data
getpower                Get the index with power restriction for
                        certain study with BH adjusted p-value and
                        certain power.
getpqsi                 Compute pooled QC linear index according to run
                        order
getrangecsv             Get a mzrt list and/or save mz and rt range as
                        csv file.
getretcor               Perform peaks list alignment and return
                        features table
getrmd                  Get the Relative Mass Defect
getsim                  output the similarity of two dataset
gettechrep              Get the report for technique replicates.
gettimegrouprep         Get the time series or two factor DoE report
                        for samples with biological and technique
                        replicates in different groups
getupload               Get the csv files from xcmsset/XCMSnExp/list
                        object
getupload2              Get the csv files to be submitted to
                        Metaboanalyst
getupload3              Get the csv files to be submitted to
                        Metaboanalyst
gifmr                   plot scatter plot for rt-mz profile and output
                        gif file for multiple groups
list                    Demo data
ma                      filter data by average moving box
matrix                  Demo raw data matrix
plotanno                Show MS/MS pmd annotation result
plotcc                  plot the calibration curve with error bar, r
                        squared and equation.
plotden                 plot the density for multiple samples
plotdwtus               plot density weighted intensity for multiple
                        samples
plote                   plot EIC and boxplot for all peaks and return
                        diffreport
plotgroup               Plot the response group of GC-MS
plothist                plot the density of the GC-MS data with EM
                        algorithm to separate the data into two log
                        normal distribution.
plothm                  Plot the heatmap of mzrt profiles
plotint                 plot the information of integration
plotintslope            plot the slope information of integration
plotkms                 plot the kendrick mass defect diagram
plotmr                  plot the scatter plot for peaks list with
                        threshold
plotmrc                 plot the diff scatter plot for peaks list with
                        threshold between two groups
plotms                  plot GC/LC-MS data as a heatmap with TIC
plotmsrt                Plot EIC of certain m/z and return dataframe
                        for integration
plotmz                  plot GC/LC-MS data as scatter plot
plotpca                 plot the PCA for multiple samples
plotpeak                plot intensity of peaks across samples or
                        samples across peaks
plotridge               plot ridgeline density plot
plotridges              Relative Log Abundance Ridge (RLAR) plots for
                        samples or peaks
plotrla                 Relative Log Abundance (RLA) plots
plotrsd                 plot the rsd influences of data in different
                        groups
plotrtms                Plot mass spectrum of certain retention time
                        and return mass spectrum vector (MSP file) for
                        NIST search
plotrug                 plot 1-d density for multiple samples
plotsms                 Plot the intensity distribution of GC-MS
plotsub                 Plot the background of data
plott                   plot GC-MS data as a heatmap for constant speed
                        of temperature rising
plottic                 Plot Total Ion Chromatogram (TIC)
qbatch                  Get the MIR from the file
runMDPlot               Shiny application for interactive mass defect
                        plots analysis
runsccp                 Shiny application for Short-Chain Chlorinated
                        Paraffins analysis
sccp                    Short-Chain Chlorinated Paraffins(SCCPs) peaks
                        information for quantitative analysis
submd                   Get the differences of two GC/LC-MS data
svabatch                Plot the influences of DoE and Batch effects on
                        each peaks
svacor                  Surrogate variable analysis(SVA) to correct the
                        unknown batch effects
svadata                 Filter the data with p value and q value
svapca                  Principal component analysis(PCA) for SVA
                        corrected data and raw data
svaplot                 Filter the data with p value and q value and
                        show them
svaupload               Get the corrected data after SVA for
                        metabolanalyst
writeMSP                Write MSP file for NIST search
xrankanno               Perform MS/MS X rank annotation for mgf file
