Man pages for jaspershen/metID
Metabolite identification based on MS1 and MS2 spectra
| annotate_result | A metIdentifyClass object. |
| construct_database | Construct in-house or public MS2 database for metID. |
| construct_massbank_database | Construct public MS2 database from massbank with msp format. |
| construct_mona_database | Construct public MS2 database from MoNA with msp format. |
| correct_database_rt | Correct RTs of metabolites in database using internal... |
| databaseClass-class | An S4 class to represent MS1 or MS2 database. |
| databaseConstruction | Construct in-house or public MS2 database for metID. |
| filter_adducts | Filter adducts. |
| filterIden | Filter identifications according to m/z error, RT error, MS... |
| filter_identification | Filter identifications according to m/z error, RT error, MS... |
| get_iden_info | Get identification information from a metIdentifyClass object |
| getIdenInfo | Get identification information from a metIdentifyClass object |
| get_identification_table | Get identification table from a metIdentifyClass object |
| getIdentificationTable | Get identification table from a metIdentifyClass object |
| getIdentificationTable2 | Get identification table from a mzIdentifyClass object |
| get_identification_table_all | get_identification_table_all |
| get_ms2_spectrum | Get MS2 spectra of peaks from databaseClass object |
| getMS2spectrum | Get MS2 spectra of peaks from databaseClass object |
| getMS2spectrum2Object | Get spectra of peaks from metIdentifyClass object |
| 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 |
| getParams | Get parameters from a metIdentifyClass object |
| getParams2 | Get parameters from a mzIdentifyClass 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 |
| identifyPeak | Identify metabolites based on MS1 or MS/MS database |
| identify_single_peak | Identify single peak based on database. |
| metID | Show the base information of metID pacakge |
| metIdentify | Identify metabolites based on MS/MS database. |
| metIdentify4all | Identify metabolites using multiple databases one time |
| metIdentifyClass-class | An S4 class to represent annotation result. |
| metIdentifyParam | Generate the parameter list for metIdentify function |
| metID_logo | Show the base information of metID pacakge |
| ms2plot | Get MS2 match plots from a metIdentifyClass object |
| msDatabase_hilic0.0.2 | Michael Snyder lab RPLC database |
| msDatabase_rplc0.0.2 | Michael Snyder lab RPLC database |
| mzIdentify | Identify peaks based on MS1 database |
| mzIdentifyParam | Generate the mzIdentify parameter list |
| read_mgf | read_mgf |
| readMGF | readMGF |
| read_mgf_experiment | read_mgf_experiment |
| read_mgf_gnps | read_mgf_gnps |
| read_mgf_mona | read_mgf_mona |
| read_msp | read_msp |
| readMSP | readMSP |
| read_msp_database | read_msp_database |
| read_msp_gnps | read_msp_gnps |
| read_msp_mona | read_msp_mona |
| readMSP_MoNA | readMSP_MoNA |
| read_mzxml | read_mzxml |
| readMZXML | readMZXML |
| rp.neg | Reverse phase negative mode adduct table |
| rp.pos | Reverse phase positive mode adduct table |
| trans2newStyle | Transform old style identification table to new style |
| trans_to_new_style | Transform old style identification table to new style |
| whichHasIden | Get the peak names which have identifications |
| which_has_identification | Get the peak names which have identifications |
| write_mgf_gnps | Export metID database to mgf (gnps format) |
| write_mgf_massbank | Export metID database to mgf (MassBank format) |
| write_mgf_mona | Export metID database to mgf (mona format) |
| write_msp_gnps | Export metID database to msp (gnps format) |
| write_msp_massbank | Export metID database to msp (MassBank format) |
| write_msp_mona | Export metID database to msp (mona format) |
