| checkGoldenRules | Check Chemical Formula against Fiehn Seven Golden Rules |
| cleanMGF | Clean an MGF file by keeping only formula-explainable peaks |
| c.mzrt | c method for mzrt object |
| 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 |
| 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... |
| getcompare | Align multiple peaks list to one peak list |
| getcsv | Convert an list object to csv file |
| getdoe | Generate the group level rsd and average intensity based on... |
| getdwtus | Density weighted intensity for one sample |
| getfilter | Filter the data based on row and column index |
| getformula | Get chemical formula for mass to charge ratio using the... |
| getHRMF | Batch High Resolution Mass Filtering for all compounds in an... |
| 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 |
| getmdh | Get the high order unit based Mass Defect |
| getmdr | Get the raw Mass Defect |
| getms1anno | Annotation of MS1 data by compounds database by predefined... |
| getMSP | read in MSP file as list for ms/ms or ms(EI) annotation |
| 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 |
| 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 |
| gifmr | plot scatter plot for rt-mz profile and output gif file for... |
| HRMF | High Resolution Mass Filtering (HRMF) for GC/LC HRMS data |
| integration | Just integrate data according to fixed rt and fixed noise... |
| list | Demo data |
| ma | filter data by average moving box |
| matrix | Demo raw data matrix |
| 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 |
| plotEIC | Plot extracted ion chromatograms from raw mzML/mzXML data |
| 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 |
| 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 |
| 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) |
| plotTopMS1Peaks | Extract top MS1 ions from MS2 EIC interactively |
| plotTopMS2Peaks | Extract top MS2 ions from MS1 EIC interactively |
| rcpp_check_golden_rules | Check Formula against Fiehn Seven Golden Rules |
| rcpp_decompose_mass | Decompose Mass into Candidate Chemical Formulas using the... |
| rcpp_decompose_masses | Decompose a Vector of Masses in Parallel using the HORIZON... |
| rcpp_get_molecule | Calculate Exact Mass and Isotope Distribution using the... |
| rcpp_score_isotopes | Calculate Isotopic Pattern Similarity Scores |
| 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... |
| scoreIsotopes | Calculate Isotopic Pattern Similarity Scores |
| TBBPA | Demo data for TBBPA metabolism in Pumpkin |
| writeMSP | Write MSP file for NIST search |
