rformassspectrometry/CompoundDb
Creating and Using (Chemical) Compound Annotation Databases

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Search the rformassspectrometry/CompoundDb package
Vignettes
Functions
196
Source code
26
Man pages
11
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rformassspectrometry/CompoundDb: Creating and Using (Chemical) Compound Annotation Databases
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API

API for rformassspectrometry/CompoundDb
Creating and Using (Chemical) Compound Annotation Databases

Global functions
$<-,MsBackendCompDb-method Man page
.add_join_tables Source code
.add_mz_range_column Source code
.append_msms_spectra Source code
.available_peaks_variables Source code
.build_query_CompDb Source code
.check_parameter_file Source code
.collapse_spectrum_df Source code
.compound_id_from_mona_sdf Source code
.copy_compdb Source code
.create_ion_table Source code
.db_file_from_metadata Source code
.dbconn Source code
.dbflags Source code
.dbname Source code
.deserialize_mz_intensity Source code
.expand_spectrum_df Source code
.extract_field_from_string Source code
.extract_spectra_mona_sdf Source code
.fetch_data Source code
.fetch_peaks Source code
.field Source code
.filter_class Source code
.from Source code
.get_property Source code
.guess_sdf_source Source code
.has_msms_spectra Source code
.import_hmdb_ms_ms_spectrum Source code
.import_lipidblast Source code
.import_lipidblast_json_chunk Source code
.import_mona_sdf Source code
.initialize_compdb Source code
.insert_msms_spectra Source code
.is_sdf_filename Source code
.join_tables Source code
.lipidblast_parallel_parse Source code
.map_spectraVariables_to_sql Source code
.map_sql_to_spectraVariables Source code
.metadata Source code
.metadata_value Source code
.msms_spectrum_add_missing_columns Source code
.order Source code
.parse_lipidblast_json_element Source code
.peaks_data Source code
.prefix_columns Source code
.prepare_msms_spectra_table Source code
.process_filter Source code
.reduce_tables Source code
.reduce_tables_start_from Source code
.require_spectra Source code
.select Source code
.simple_extract_compounds_sdf Source code
.spectra_data Source code
.sql_condition Source code
.sql_logicOp Source code
.sql_value Source code
.supported_filters Source code
.tables Source code
.throw_error Source code
.validCompDb Source code
.validIonDb Source code
.valid_compound Source code
.valid_data_frame_columns Source code
.valid_dbcon Source code
.valid_metadata Source code
.valid_msms_spectrum Source code
.where Source code
.where_filter Source code
CompDb Man page Source code
CompDb-class Man page
CompoundIdFilter Man page Source code
CompoundIdFilter-class Man page
ExactmassFilter Man page Source code
ExactmassFilter-class Man page
Filter-classes Man page
FormulaFilter Man page Source code
FormulaFilter-class Man page
InchiFilter Man page Source code
InchiFilter-class Man page
InchikeyFilter Man page Source code
InchikeyFilter-class Man page
IonAdductFilter Man page Source code
IonAdductFilter-class Man page
IonDb Man page
IonDb,CompDb,missing-method Man page
IonDb,DBIConnection,CompDb-method Man page
IonDb,DBIConnection,missing-method Man page
IonDb,character,CompDb-method Man page
IonDb,character,missing-method Man page
IonDb,missing,missing-method Man page
IonDb-class Man page
IonIdFilter Man page Source code
IonIdFilter-class Man page
IonMzFilter Man page Source code
IonMzFilter-class Man page
IonRtFilter Man page Source code
IonRtFilter-class Man page
MsBackendCompDb Man page Source code
MsBackendCompDb-class Man page
MsmsMzRangeMaxFilter Man page Source code
MsmsMzRangeMaxFilter-class Man page
MsmsMzRangeMinFilter Man page Source code
MsmsMzRangeMinFilter-class Man page
NameFilter Man page Source code
NameFilter-class Man page
Spectra,CompDb-method Man page
SpectrumIdFilter Man page Source code
SpectrumIdFilter-class Man page
[,MsBackendCompDb,ANY-method Man page
backendBpparam,MsBackendCompDb-method Man page
backendInitialize,MsBackendCompDb-method Man page
compoundVariables Man page
compoundVariables,CompDb-method Man page
compound_tbl_lipidblast Man page Source code
compound_tbl_sdf Man page Source code
compounds,CompDb-method Man page
copyCompDb Man page Source code
createCompDb Man page Source code
createCompDbPackage Man page Source code
dataStorage,MsBackendCompDb-method Man page
dbconn,CompDb-method Man page
deleteCompound Man page
deleteCompound,CompDb-method Man page
deleteCompound,IonDb-method Man page
deleteIon Man page
deleteIon,IonDb-method Man page
deleteSpectra Man page
deleteSpectra,CompDb-method Man page
emptyCompDb Man page Source code
expandMzIntensity Man page Source code
extractByIndex,MsBackendCompDb,ANY-method Man page
hasMsMsSpectra Man page Source code
import_mona_sdf Man page Source code
insertCompound Man page
insertCompound,CompDb-method Man page
insertIon Man page
insertIon,IonDb-method Man page
insertSpectra Man page
insertSpectra,CompDb,Spectra-method Man page
intensity<-,MsBackendCompDb-method Man page
ionVariables Man page
ionVariables,IonDb-method Man page
ions Man page
ions,IonDb-method Man page
make_metadata Man page Source code
mass2mz Man page
mass2mz,ANY-method Man page
mass2mz,CompDb-method Man page
metadata,CompDb-method Man page
msms_spectra_hmdb Man page Source code
msms_spectra_mona Man page Source code
mz<-,MsBackendCompDb-method Man page
peaksData,MsBackendCompDb-method Man page
peaksVariables,MsBackendCompDb-method Man page
precScanNum,MsBackendCompDb-method Man page
show Man page
show,CompDb-method Man page
show,IonDb-method Man page
show,MsBackendCompDb-method Man page
spectraData,MsBackendCompDb-method Man page
spectraNames,MsBackendCompDb-method Man page
spectraNames<-,MsBackendCompDb-method Man page
spectraVariables,CompDb-method Man page
src_compdb Man page Source code
supportedFilters,CompDb-method Man page
tables Man page Source code
tic,MsBackendCompDb-method Man page
rformassspectrometry/CompoundDb documentation built on June 2, 2025, 1:16 a.m.

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