# Creating and Using (Chemical) Compound Annotation Databases

## Documentation for package ‘CompoundDb’ version 1.12.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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
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