Function reference
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CompDb()
hasMsMsSpectra()
src_compdb()
tables()
copyCompDb()
dbconn(<CompDb>)
Spectra(<CompDb>)
supportedFilters(<CompDb>)
metadata(<CompDb>)
spectraVariables(<CompDb>)
compoundVariables(<CompDb>)
compounds(<CompDb>)
insertSpectra(<CompDb>,<Spectra>)
deleteSpectra(<CompDb>)
mass2mz(<CompDb>)
insertCompound(<CompDb>)
deleteCompound(<CompDb>)
- Simple compound (metabolite) databases
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CompoundIdFilter()
SpectrumIdFilter()
NameFilter()
MsmsMzRangeMinFilter()
MsmsMzRangeMaxFilter()
ExactmassFilter()
FormulaFilter()
InchiFilter()
InchikeyFilter()
IonIdFilter()
IonAdductFilter()
IonMzFilter()
IonRtFilter()
- Filters supported by CompDb and IonDb
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ionVariables(<IonDb>)
ions(<IonDb>)
insertIon(<IonDb>)
deleteIon(<IonDb>)
IonDb(<missing>,<missing>)
IonDb(<character>,<missing>)
IonDb(<CompDb>,<missing>)
IonDb(<DBIConnection>,<missing>)
IonDb(<character>,<CompDb>)
IonDb(<DBIConnection>,<CompDb>)
- IonDb: compound database with additional ion information
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MsBackendCompDb()
backendInitialize(<MsBackendCompDb>)
show(<MsBackendCompDb>)
peaksData(<MsBackendCompDb>)
peaksVariables(<MsBackendCompDb>)
dataStorage(<MsBackendCompDb>)
`intensity<-`(<MsBackendCompDb>)
`mz<-`(<MsBackendCompDb>)
spectraData(<MsBackendCompDb>)
spectraNames(<MsBackendCompDb>)
`spectraNames<-`(<MsBackendCompDb>)
`[`(<MsBackendCompDb>,<ANY>)
`$<-`(<MsBackendCompDb>)
precScanNum(<MsBackendCompDb>)
tic(<MsBackendCompDb>)
backendBpparam(<MsBackendCompDb>)
- CompDb-based MS spectrum backend
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compound_tbl_lipidblast()
- Extract compound data from LipidBlast
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compound_tbl_sdf()
- Extract compound data from a file in SDF format
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createCompDb()
createCompDbPackage()
make_metadata()
emptyCompDb()
- Create a CompDb database
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expandMzIntensity()
- Expand m/z and intensity values in a data.frame
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import_mona_sdf()
- Import compound and spectrum information from MoNa
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msms_spectra_hmdb()
- Import MS/MS spectra from HMDB xml files
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msms_spectra_mona()
- Import MS/MS spectra from MoNa