Package index • metid

All functions
`annotate_metabolites()`	Annotate Metabolites
`annotate_metabolites_mass_dataset()`	Annotate Metabolites in a mass_dataset Object
`annotate_peaks_mz_rt_ms2()`	Annotate Peaks Based on MS1, Retention Time (RT), and MS2
`annotate_single_peak_mass_dataset()`	Annotate a Single Peak in a mass_dataset Object
`calculate_confidence_level()`	Calculate Confidence Level for Metabolite Annotations
`calculate_dotproduct()`	Calculate Dot Product Score for MS2 Spectra
`calculate_ms2_matching_score()`	Calculate MS2 Spectra Matching Score
`calculate_mz_match_score()`	Calculate m/z Match Score
`calculate_rt_match_score()`	Calculate Retention Time (RT) Match Score
`calculate_total_score()`	Calculate the Total Annotation Score
`check_adduct_table()`	Validate the Adduct Table
`check_database()`	Validate a Database Object for Metabolite Annotation
`check_mass_dataset()`	Validate the mass_dataset Object for Metabolite Annotation
`check_ms1_ms2_info()`	Validate MS1 and MS2 Information
`check_parameters4annotate_metabolites()`	Validate Parameters for Metabolite Annotation
`check_parameters4calculate_total_score()`	Validate Parameters for Calculating Total Score
`construct_database()`	Construct a Mass Spectra Database
`construct_massbank_database()`	Construct a Spectral Database from MassBank Data
`construct_mona_database()`	Construct a Spectral Database from MoNA Data
`correct_database_rt()`	Correct Retention Time (RT) in a Spectral Database
`databaseClass-class`	Class for Managing Spectral Database Information
`extract_database_name()`	Extract the Name of the Database
`extract_ms1_database()`	Extract MS1 Information from a Database
`extract_ms1_info()`	Extract MS1 Information from a mass_dataset Object
`extract_ms2_database()`	Extract MS2 Spectra from a Database
`extract_ms2_info()`	Extract MS2 Information from a mass_dataset Object
`filter_adducts()`	Filter adducts.
`filter_identification()`	Filter identifications according to m/z error, RT error, MS similarity and total score
`getIdentificationTable2()`	Get identification table from a mzIdentifyClass object
`getMS2spectrum()`	Get MS2 spectra of peaks from databaseClass object
`get_iden_info()`	Get identification information from a metIdentifyClass object
`get_identification_table()`	Get identification table from a metIdentifyClass object
`get_identification_table_all()`	get_identification_table_all
`get_ms2_spectrum()`	Retrieve MS2 Spectrum from a Database
`get_ms2_spectrum_from_object()`	Get spectra of peaks from metIdentifyClass object
`get_parameters()`	Get parameters from a metIdentifyClass object
`get_parameters_metid()`	Get parameters from a metIdentifyClass object
`hilic.neg`	HILIC negative mode adduct table
`hilic.pos`	HILIC positive mode adduct table
`identify_metabolite_all()`	Identify metabolites using multiple databases one time
`identify_metabolites()`	Identify metabolites based on MS1 or MS/MS database
`identify_metabolites_params()`	Generate the parameter list for identify_metabolites function
`identify_ms2_only()`	Identify metabolites based on MS/MS database
`identify_peak()`	Identify a Peak in a Mass Spectrometry Dataset
`identify_single_peak()`	Identify single peak based on database.
`load_adduct_table()`	Load the Adduct Table Based on Polarity and Column Type
`match_ms2_fragments()`	Match MS2 Fragments Between Experimental and Library Spectra
`match_ms2_temp()`	Match MS2 Spectra to Database Compounds
`metIdentification()`	Metabolite Identification Using MS1 and MS2 Data
`metIdentify()`	Identify metabolites based on MS/MS database.
`metIdentifyClass-class`	An S4 class to represent annotation result.
`metIdentify_mass_dataset()`	Metabolite Identification in a mass_dataset Object Using MS1 and MS2 Data
`metid()`	Show the base information of metid pacakge
`metid_conflicts()`	Conflicts between the metid and other packages
`metid_logo()`	Display the metid Logo and Information
`metid_packages()`	List all packages in the metid
`ms2_plot_mass_dataset()`	Plot MS2 Spectra for a Single Peak in a mass_dataset Object
`ms2plot()`	Get MS2 match plots from a metIdentifyClass object
`msDatabase_hilic0.0.2`	Michael Snyder lab RPLC database 0.0.2
`msDatabase_rplc0.0.2`	Michael Snyder lab RPLC database 0.0.2
`mzIdentify()`	Identify peaks based on MS1 database
`mzIdentifyParam()`	Generate the mzIdentify parameter list
`mzIdentify_mass_dataset()`	Metabolite Identification in a mass_dataset Object Using MS1 Data
`orbitrap_database0.0.3`	orbitrap_database0.0.3
`plot_ms2_matching()`	Plot MS2 Matching Between Experimental and Library Spectra
`readMGF()`	readMGF
`readMSP()`	readMSP
`readMSP_MoNA()`	readMSP_MoNA
`readMZXML()`	readMZXML
`read_mgf_experiment()`	Read MGF Data from Experimental Files
`read_mgf_gnps()`	This function reads Mass Spectrometry (MS) data in MGF format from GNPS, extracts the MS2 spectra, and returns it in a structured format.
`read_mgf_mona()`	Read MGF Data from MoNA
`read_msp()`	Read MSP Data
`read_msp_database()`	Read MSP Database
`read_msp_gnps()`	————————————————————————— Read MSP Data from GNPS
`read_msp_mona()`	————————————————————————— Read MSP Data from MoNA
`remove_impossible_annotations()`	Remove Impossible Annotations Based on Adducts
`remove_noise()`	Remove Noise from MS2 Spectrum
`rp.neg`	Reverse phase negative mode adduct table
`rp.pos`	Reverse phase positive mode adduct table
`snyder_database_hilic0.0.3`	Michael Snyder lab RPLC database
`snyder_database_rplc0.0.3`	Michael Snyder lab RPLC database
`colnames(<databaseClass>)` `nrow(<databaseClass>)` `ncol(<databaseClass>)` `dim(<databaseClass>)`	colnames
`summary_annotation_table()`	Summary of Annotation Table with Plot
`trans_to_new_style()`	Transform old style identification table to new style
`which_has_identification()`	Get the peak names which have identifications
`write_mgf_gnps()`	Write GNPS Spectra to MGF Format
`write_mgf_massbank()`	Write MassBank Spectra to MGF Format
`write_mgf_mona()`	Write MoNA Spectra to MGF Format
`write_msp()`	Write MSP Data to a File
`write_msp_gnps()`	Write GNPS Spectra to MSP Format
`write_msp_massbank()`	Write MassBank Spectra to MSP Format
`write_msp_mona()`	Write MoNA Spectra to MSP Format

Reference

All functions