| batch | Get the MIR and related information from the files |
| cbmd | Combine two data with similar retention time while different... |
| dotpanno | Perform MS/MS dot product annotation for mgf file |
| enviGCMS-deprecated | Deprecated functions in package 'enviGCMS'. |
| findline | find line of the regression model for GC-MS |
| findlipid | Find lipid class of metabolites base on referenced Kendrick... |
| findmet | Screen metabolites by Mass Defect |
| findohc | Screen organohalogen compounds by retention time, mass defect... |
| findpfc | Find PFCs based on mass defect analysis |
| getalign | Align two peaks vectors by mass to charge ratio and/or... |
| getalign2 | Align mass to charge ratio and/or retention time to remove... |
| getarea | Get the peak information from samples for SCCPs detection |
| getareastd | Get the peak information from SCCPs standards |
| 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... |
| getdoe | Generate the group level rsd and average intensity based on... |
| getdwtus | Density weighted intensity for one sample |
| getfeaturesanova | Get the features from anova, with p value, q value, rsd and... |
| getfeaturest | Get the features from t test, with p value, q value, rsd and... |
| 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... |
| getimputation | Impute the peaks list data |
| GetIntegration | GetIntegration was mainly used for get the integration of... |
| Getisotopologues | Get the selected isotopologues at certain MS data |
| getmass | Get the exact mass of the isotopologues from a chemical... |
| getmassdefect | Get mass defect with certain scaled factor |
| getmd | Import data and return the annotated matrix for GC/LC-MS by... |
| 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... |
| getms1anno | Annotation of MS1 data by compounds database by predefined... |
| getMSP | read in MSP file as list for ms/ms or ms(EI) annotation |
| getmzrt | Get the mzrt profile and group information as a mzrt list... |
| getmzrt2 | Get the mzrt profile and group information for batch... |
| 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... |
| getpqsi | Compute pooled QC linear index according to run order |
| getQCraw | get the data of QC compound for a group of data |
| 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 |
| getsccp | Quantitative analysis for short-chain chlorinated... |
| 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... |
| 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... |
| Integration | Just integrate data according to fixed rt and fixed noise... |
| list | Demo data |
| ma | filter data by average moving box |
| Mode | define the Mode function |
| plotanno | Show MS/MS pmd annotation result |
| plotcc | plot the calibration curve with error bar, r squared and... |
| 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... |
| 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... |
| 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... |
| plotridge | plot ridgeline density plot |
| plotridges | Relative Log Abundance Ridge (RLAR) plots for samples or... |
| 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... |
| 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... |
| 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... |
| sccp | Short-Chain Chlorinated Paraffins(SCCPs) peaks information... |
| 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... |
| svadata | Filter the data with p value and q value |
| svapca | Principal component analysis(PCA) for SVA corrected data and... |
| svaplot | Filter the data with p value and q value and show them |
| svaupload | Get the corrected data after SVA for metabolanalyst |
| TBBPA | Demo data for TBBPA metabolism in Pumpkin |
| writeMSP | Write MSP file for NIST search |
| xrankanno | Perform MS/MS X rank annotation for mgf file |
