Function reference

All functions

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

CompoundIdFilter() SpectrumIdFilter() NameFilter() MsmsMzRangeMinFilter() MsmsMzRangeMaxFilter() ExactmassFilter() FormulaFilter() InchiFilter() InchikeyFilter() IonIdFilter() IonAdductFilter() IonMzFilter() IonRtFilter()

Filters supported by CompDb and IonDb

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

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

compound_tbl_lipidblast()

Extract compound data from LipidBlast

compound_tbl_sdf()

Extract compound data from a file in SDF format

createCompDb() createCompDbPackage() make_metadata() emptyCompDb()

Create a CompDb database

expandMzIntensity()

Expand m/z and intensity values in a data.frame

import_mona_sdf()

Import compound and spectrum information from MoNa

msms_spectra_hmdb()

Import MS/MS spectra from HMDB xml files

msms_spectra_mona()

Import MS/MS spectra from MoNa