Creating and Using (Chemical) Compound Annotation Databases
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Documentation for package ‘CompoundDb’ version 1.12.0
Help Pages
| $<--method | CompDb-based MS spectrum backend |
| backendBpparam-method | CompDb-based MS spectrum backend |
| backendInitialize-method | CompDb-based MS spectrum backend |
| CompDb | Simple compound (metabolite) databases |
| CompDb-class | Simple compound (metabolite) databases |
| CompoundIdFilter | Filters supported by CompDb and IonDb |
| CompoundIdFilter-class | Filters supported by CompDb and IonDb |
| compounds-method | Simple compound (metabolite) databases |
| compoundVariables | Simple compound (metabolite) databases |
| compoundVariables-method | Simple compound (metabolite) databases |
| compound_tbl_lipidblast | Extract compound data from LipidBlast |
| compound_tbl_sdf | Extract compound data from a file in SDF format |
| copyCompDb | Simple compound (metabolite) databases |
| createCompDb | Create a CompDb database |
| createCompDbPackage | Create a CompDb database |
| dataStorage-method | CompDb-based MS spectrum backend |
| dbconn-method | Simple compound (metabolite) databases |
| deleteCompound | Simple compound (metabolite) databases |
| deleteCompound-method | Simple compound (metabolite) databases |
| deleteIon | IonDb: compound database with additional ion information |
| deleteIon-method | IonDb: compound database with additional ion information |
| deleteSpectra | Simple compound (metabolite) databases |
| deleteSpectra-method | Simple compound (metabolite) databases |
| emptyCompDb | Create a CompDb database |
| ExactmassFilter | Filters supported by CompDb and IonDb |
| ExactmassFilter-class | Filters supported by CompDb and IonDb |
| expandMzIntensity | Expand m/z and intensity values in a data.frame |
| extractByIndex-method | CompDb-based MS spectrum backend |
| Filter-classes | Filters supported by CompDb and IonDb |
| FormulaFilter | Filters supported by CompDb and IonDb |
| FormulaFilter-class | Filters supported by CompDb and IonDb |
| hasMsMsSpectra | Simple compound (metabolite) databases |
| import_mona_sdf | Import compound and spectrum information from MoNa |
| InchiFilter | Filters supported by CompDb and IonDb |
| InchiFilter-class | Filters supported by CompDb and IonDb |
| InchikeyFilter | Filters supported by CompDb and IonDb |
| InchikeyFilter-class | Filters supported by CompDb and IonDb |
| insertCompound | Simple compound (metabolite) databases |
| insertCompound-method | Simple compound (metabolite) databases |
| insertIon | IonDb: compound database with additional ion information |
| insertIon-method | IonDb: compound database with additional ion information |
| insertSpectra | Simple compound (metabolite) databases |
| insertSpectra-method | Simple compound (metabolite) databases |
| intensity<--method | CompDb-based MS spectrum backend |
| IonAdductFilter | Filters supported by CompDb and IonDb |
| IonAdductFilter-class | Filters supported by CompDb and IonDb |
| IonDb | IonDb: compound database with additional ion information |
| IonDb-class | IonDb: compound database with additional ion information |
| IonDb-method | IonDb: compound database with additional ion information |
| IonIdFilter | Filters supported by CompDb and IonDb |
| IonIdFilter-class | Filters supported by CompDb and IonDb |
| IonMzFilter | Filters supported by CompDb and IonDb |
| IonMzFilter-class | Filters supported by CompDb and IonDb |
| IonRtFilter | Filters supported by CompDb and IonDb |
| IonRtFilter-class | Filters supported by CompDb and IonDb |
| ions | IonDb: compound database with additional ion information |
| ions-method | IonDb: compound database with additional ion information |
| ionVariables | IonDb: compound database with additional ion information |
| ionVariables-method | IonDb: compound database with additional ion information |
| make_metadata | Create a CompDb database |
| mass2mz | Simple compound (metabolite) databases |
| mass2mz-method | Simple compound (metabolite) databases |
| metadata-method | Simple compound (metabolite) databases |
| MsBackendCompDb | CompDb-based MS spectrum backend |
| MsBackendCompDb-class | CompDb-based MS spectrum backend |
| MsmsMzRangeMaxFilter | Filters supported by CompDb and IonDb |
| MsmsMzRangeMaxFilter-class | Filters supported by CompDb and IonDb |
| MsmsMzRangeMinFilter | Filters supported by CompDb and IonDb |
| MsmsMzRangeMinFilter-class | Filters supported by CompDb and IonDb |
| msms_spectra_hmdb | Import MS/MS spectra from HMDB xml files |
| msms_spectra_mona | Import MS/MS spectra from MoNa |
| mz<--method | CompDb-based MS spectrum backend |
| NameFilter | Filters supported by CompDb and IonDb |
| NameFilter-class | Filters supported by CompDb and IonDb |
| peaksData-method | CompDb-based MS spectrum backend |
| peaksVariables-method | CompDb-based MS spectrum backend |
| precScanNum-method | CompDb-based MS spectrum backend |
| show | Simple compound (metabolite) databases |
| show-method | Simple compound (metabolite) databases |
| show-method | IonDb: compound database with additional ion information |
| show-method | CompDb-based MS spectrum backend |
| Spectra-method | Simple compound (metabolite) databases |
| spectraData-method | CompDb-based MS spectrum backend |
| spectraNames-method | CompDb-based MS spectrum backend |
| spectraNames<--method | CompDb-based MS spectrum backend |
| spectraVariables-method | Simple compound (metabolite) databases |
| SpectrumIdFilter | Filters supported by CompDb and IonDb |
| SpectrumIdFilter-class | Filters supported by CompDb and IonDb |
| src_compdb | Simple compound (metabolite) databases |
| supportedFilters-method | Simple compound (metabolite) databases |
| tables | Simple compound (metabolite) databases |
| tic-method | CompDb-based MS spectrum backend |
| [-method | CompDb-based MS spectrum backend |