GetIntegration          GetIntegration was mainly used for get the
                        intergration of certain ion's chromatogram data
                        and plot the data
Getisotopologues        Get the selected isotopologues at certain MS
                        data
Integration             Just intergrate data according to fixed rt and
                        fixed noise area
batch                   Get the MIR and related information from the
                        files
cbmd                    Combine two data with similar retention time
                        while different mass range
findline                find line of the regression model for GC-MS
getQCraw                get the data of QC compound for a group of data
getbgremove             Get the peak list with blank samples' peaks
                        removed
getbiotechrep           Get the report for biological replicates.
getdata                 Get xcmsset object in one step with optimized
                        methods.
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
getgrouprep             Get the report for samples with biological and
                        technique replicates in different groups
getmassdefect           Get mass defect with certain scaled factor
getmassdiff             Isotope extraction for single group of samples
                        with certain mass diff
getmd                   Import data and return the annotated matrix for
                        GC/LC-MS by m/z range and retention time
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 to be submitted to
                        Metaboanalyst
ma                      filter data by average moving box
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 seperate the data into two log
                        normal distribution.
plotint                 plot the information of intergretion
plotintslope            plot the slope information of intergretion
plotkms                 plot the kendrick mass defect diagram
plotmr                  plot the scatter plot for xcmsset (or two)
                        objects with threshold
plotmrc                 plot the diff scatter plot for one xcmsset
                        objects with threshold and two groups
plotms                  plot GC/LC-MS data as a heatmap with TIC
plotmsrt                Plot EIC of certain m/z and return dataframe
                        for intergration
plotmz                  plot GC/LC-MS data as scatter plot
plotpca                 plot the PCA of xcmsset
plotrsd                 plot the rsd influnces of data
plotrtms                Plot mass spectrum of certain retention time
                        and return mass spectrum vector (MSP file) for
                        NIST search
plotsms                 Plot the intensity distribution of GC-MS
plotsub                 Plot the backgrond 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
submd                   Get the differences of two GC/LC-MS data
svabatch                Plot the influnces 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 files for NIST search
