| acylcerdb | AcylCeramides database |
| adductsTable | Adducts table |
| alignmsbatch | Align samples from an msbatch |
| annotateIsotopes | Annotate isotopes |
| annotatemsbatch | Lipid annotation for an msbatch |
| assignDB | Load LipidMS default data bases |
| baconjdb | Bile acids conjugates database |
| badb | Bile acids database |
| batchdataProcessing | Process several mzXML files (peakpicking and isotope... |
| carnitinesdb | Carnitines database |
| cbs | Total number of carbons and double bounds |
| CEdb | CEs database |
| cerdb | Ceramides database |
| cerPdb | Ceramides Phosphate database |
| chainFrags | Search of chain specific fragments |
| chains | extract chains composition from a lipid name |
| checkClass | Search of class fragments to confirm the lipid class. |
| checkIntensityRules | Check intensity rules |
| checkIntRules | Check intensity rules |
| cldb | Cardiolipins database |
| clust | Clustering for MS peaks based on mz or RT. |
| clustdist | Calculate max distance between clusters. |
| clustering | EIC extraction based on previous partitions generated by... |
| coelutingFrags | Coeluting fragments extraction |
| coelutionScore | calculate coelution score between two peaks |
| combineChains | Combine chain fragments that could belong to the same... |
| confLevels | Confidence Annotation Levels |
| createLipidDB | Customizable lipid DBs creator |
| crossAdducts | Cross different candidates tables to remove false positives. |
| crossTables | Cross the original MS1 peaklist with the annotation results |
| dataProcessing | Process mzXML files individually: peakpicking and isotope... |
| dbFourChains | Creation of a database for C. |
| dbOneChain | Creation of a database for Carnitines, CE, FA, HFA, LPL, MG,... |
| dbSphingolipids | Creation of a database for Cer, CerP, GlcCer and SM |
| dbThreeChains | Creation of a database for TG. |
| dbTwoChains | Creation of a database for FAHFA, DG and PL. |
| ddaFrags | MS/MS scan extraction of a precursor in DDA |
| dgdb | DGs database |
| diffcb | Difference between two carbon:bounds structures |
| fadb | FAs database |
| fahfadb | FAHFAs database |
| fillpeaksmsbatch | Fill peaks from a grouped msbatch |
| filtermsms | Presence or absence of an mz value within a vector of mz... |
| filtrateAdducts | Remove low adduct supported candidates to avoid false... |
| findCandidates | Search of lipid candidates of a certain class |
| findMS2precursor | find lisnks between MS1 peaks and precursors selected for MS2... |
| findPrecursor | Find candidate precursor from fullMS function |
| frags | Search for fragments of interest withing a list of coeluting... |
| getallpeaks | Extract peaks from all msobjects in a msbatch. |
| getfeaturestable | Write features table based on groups |
| getFormula | Get formula and neutral mass for annotated compounds |
| getInclusionList | Obtain an inclusion list from the annotation results |
| groupmsbatch | Group features from an msbatch |
| hfadb | HFAs database |
| idAcylCerneg | Acylceramides (AcylCer) annotation for ESI- |
| idAcylCerpos | Acylceramides (AcylCer) annotation for ESI+ |
| idBAneg | Bile Acids (BA) annotation for ESI- |
| idCarpos | Acylcarnitine annotation for ESI+ |
| idCEpos | Cholesteryl Esters (CE) annotation for ESI+ |
| idCerneg | Ceramides (Cer) annotation for ESI- |
| idCerPneg | Ceramides phosphate (CerP) annotation for ESI- |
| idCerpos | Ceramides (Cer) annotation for ESI+ |
| idCerPpos | Ceramides phosphate (CerP) annotation for ESI+ |
| idCLneg | Cardiolipines (CL) annotation for ESI- |
| idDGpos | Diacylglycerols (DG) annotation for ESI+ |
| idFAHFAneg | FAHFA annotation for ESI- |
| idFAneg | Fatty Acids (FA) annotation for ESI- |
| idLPCneg | Lysophosphocholines (LPC) annotation for ESI- |
| idLPCpos | Lysophosphocholines (LPC) annotation for ESI+ |
| idLPEneg | Lysophosphoethanolamines (LPE) annotation for ESI- |
| idLPEpos | Lysophosphoethanolamines (LPE) annotation for ESI+ |
| idLPGneg | Lysophosphoglycerols (LPG) annotation for ESI- |
| idLPIneg | Lysophosphoinositols (LPI) annotation for ESI- |
| idLPSneg | Lysophosphoserines (LPS) annotation for ESI- |
| idMGpos | Monoacylglycerol (MG) annotation for ESI+ |
| idNEG | Lipids annotation for ESI- |
| idPCneg | Phosphocholines (PC) annotation for ESI- |
| idPConeg | Plasmanyl Phosphocholines (PCo) annotation for ESI- |
| idPCopos | Plasmanyl Phosphocholines (PCo) annotation for ESI+ |
| idPCpneg | Plasmenyl Phosphocholines (PCp) annotation for ESI- |
| idPCpos | Phosphocholines (PC) annotation for ESI+ |
| idPCppos | Plasmenyl Phosphocholines (PCp) annotation for ESI+ |
| idPEneg | Phosphoethanolamines (PE) annotation for ESI- |
| idPEoneg | Plasmanyl Phosphoethanolamines (PEo) annotation for ESI- |
| idPEopos | Plasmanyl Phosphoethanolamines (PEo) annotation for ESI+ |
| idPEpneg | Plasmenyl Phosphoethanolamines (PEp) annotation for ESI- |
| idPEpos | Phosphoethanolamines (PE) annotation for ESI+ |
| idPEppos | Plasmenyl Phosphoethanolamines (PEp) annotation for ESI+ |
| idPGneg | Phosphoglycerols (PG) annotation for ESI- |
| idPGpos | Phosphoglycerols (PG) annotation for ESI+ |
| idPIneg | Phosphoinositols (PI) annotation for ESI- |
| idPIpos | Phosphoinositols (PI) annotation for ESI+ |
| idPOS | Lipids annotation for ESI+ |
| idPSneg | Phosphoserines (PS) annotation for ESI- |
| idSMneg | Sphingomyelines (SM) annotation for ESI- |
| idSMpos | Sphyngomyelines (SM) annotation for ESI+ |
| idSphneg | Sphingoid bases (Sph) annotation for ESI- |
| idSphPneg | Sphingoid bases phosphate (SphP) annotation for ESI- |
| idSphpos | Sphingoid bases (Sph) annotation for ESI- |
| idSphPpos | Sphingoid bases phosphate (SphP) annotation for ESI+ |
| idTGpos | Triacylglycerols (TG) annotation for ESI+ |
| indexrtpart | Index partitions or clusters assigned during alignment. |
| joinAnnotationResults | Summarize annotation results from an msbatch into the... |
| joinfrags | Join fragments information when several peaks of the same... |
| LipidMSapp | LipidMS shiny app |
| lysopadb | LPAs database |
| lysopaodb | O-LPA database |
| lysopcdb | LPCs database |
| lysopcodb | O-LPC database |
| lysopcpdb | P-LPC database |
| lysopedb | LPEs database |
| lysopeodb | O-LPE database |
| lysopepdb | P-LPE database |
| lysopgdb | LPGs database |
| lysopidb | LPIs database |
| lysopsdb | LPSs database |
| MassAcylCer | Calculate formula and mass of acylceramides |
| MassCarnitines | Calculate formula and mass of carnitines |
| MassCE | Calculate formula and mass of cholesterol esthers |
| MassCer | Calculate formula and mass of ceramides |
| MassCerP | Calculate formula and mass of ceramides phosphate |
| MassCL | Calculate formula and mass of CL |
| MassDG | Calculate formula and mass of DG |
| MassFA | Calculate formula and mass of fatty acids |
| MassFAHFA | Calculate formula and mass of FAHFA |
| MassGlcCer | Calculate formula and mass of glucoceramides |
| MassHFA | Calculate formula and mass of hydroxi fatty acids |
| MassLysoPA | Calculate formula and mass of LPA |
| MassLysoPAo | Calculate formula and mass of LPAo |
| MassLysoPC | Calculate formula and mass of LysoPC |
| MassLysoPCo | Calculate formula and mass of LysoPCo |
| MassLysoPCp | Calculate formula and mass of LysoPCp |
| MassLysoPE | Calculate formula and mass of LPE |
| MassLysoPEo | Calculate formula and mass of LPEo |
| MassLysoPEp | Calculate formula and mass of LPEp |
| MassLysoPG | Calculate formula and mass of LPG |
| MassLysoPI | Calculate formula and mass of LPI |
| MassLysoPS | Calculate formula and mass of LysoPS |
| MassMG | Calculate formula and mass of MG |
| MassPA | Calculate formula and mass of PA |
| MassPC | Calculate formula and mass of PC |
| MassPCo | Calculate formula and mass of PCo |
| MassPCp | Calculate formula and mass of PCp |
| MassPE | Calculate formula and mass of PE |
| MassPEo | Calculate formula and mass of plasmanyl PE |
| MassPEp | Calculate formula and mass of plasmenyl PE |
| MassPG | Calculate formula and mass of PG |
| MassPI | Calculate formula and mass of PI |
| MassPIP | Calculate formula and mass of PIP |
| MassPIP2 | Calculate formula and mass of PIP2 |
| MassPIP3 | Calculate formula and mass of PIP3 |
| MassPS | Calculate formula and mass of PS |
| MassSM | Calculate formula and mass of sphingomyelines |
| MassSph | Calculate formula and mass of sphingoid bases |
| MassSphP | Calculate formula and mass of sphingoid phosphate bases |
| MassTG | Calculate formula and mass of TG |
| mgdb | MGs database |
| mzMatch | mz match withing a vector of mz values |
| nlsphdb | Neutral losses db for sphingoid bases. It is employed by... |
| organizeResults | Prepare output for LipidMS annotation functions |
| padb | PAs database |
| partitioning | agglomarative partitioning for LC-HRMS data based on enviPick... |
| pcdb | PCs database |
| pcodb | O-PC database |
| pcpdb | P-PC database |
| peakdetection | peak-pick based on previous EIC clusters generated by... |
| pedb | PEs database |
| peodb | O-PE database |
| pepdb | P-PE database |
| pgdb | PGs database |
| pidb | PIs database |
| ploteicmsbatch | EIC for all samples in a msbatch |
| plotLipids | Plot informative peaks for lipid annotation |
| plotticmsbatch | TIC for all samples in a msbatch |
| psdb | PSs database |
| readMSfile | Read mzXML file and initiate msobject |
| rtcorrection | Correct RT based on a rtmodel. |
| rtdevplot | Plot retention time deviation |
| searchIsotopes | Targeted isotopes search |
| searchIsotopesmsbatch | Targeted isotopes search for msbatch |
| select | Check matches between chains composition and precursor... |
| setmsbatch | Create msbatch for batch processing. |
| smdb | SMs database |
| sphdb | Sphingoid bases database |
| sphPdb | Sphingoid bases phosphate database |
| sumChains | Calculate total number of carbons and double bounds of lipid... |
| tgdb | TGs database |
