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C D E F G I L M N P R S T misc
| MSGFplus-package | An interface between R and MS-GF+ |
| chargeRange | Get and set the charge range in msgfPar objects |
| chargeRange-method | Get and set the charge range in msgfPar objects |
| chargeRange<- | Get and set the charge range in msgfPar objects |
| chargeRange<--method | Get and set the charge range in msgfPar objects |
| db | Get and set database in msgfPar objects |
| db-method | Get and set database in msgfPar objects |
| db<- | Get and set database in msgfPar objects |
| db<--method | Get and set database in msgfPar objects |
| enzyme | Get and set enzyme in msgfPar objects |
| enzyme-method | Get and set enzyme in msgfPar objects |
| enzyme<- | Get and set enzyme in msgfPar objects |
| enzyme<--method | Get and set enzyme in msgfPar objects |
| finished | A class referencing an asynchronous execution of MS-GF+ |
| finished-method | A class referencing an asynchronous execution of MS-GF+ |
| fragmentation | Get and set fragmentation in msgfPar objects |
| fragmentation-method | Get and set fragmentation in msgfPar objects |
| fragmentation<- | Get and set fragmentation in msgfPar objects |
| fragmentation<--method | Get and set fragmentation in msgfPar objects |
| getMSGFpar | Get a string representation of an msgfPar-related object |
| getMSGFpar-method | A class to contain parameters used in an MS-GF+ analysis |
| getMSGFpar-method | A class handling charge ranges |
| getMSGFpar-method | A class handling enzyme selection |
| getMSGFpar-method | A class handling Fragmentation types |
| getMSGFpar-method | A class handling instrument types |
| getMSGFpar-method | A class handling isotope errors |
| getMSGFpar-method | A class handling length ranges |
| getMSGFpar-method | A class handling number of matches |
| getMSGFpar-method | A class handling modification characteristics |
| getMSGFpar-method | A class handling a list of modifications |
| getMSGFpar-method | A class handling cleavage specificity |
| getMSGFpar-method | A class handling protocol choice |
| getMSGFpar-method | A class handling use of target-decoy approach for FDR estimation |
| getMSGFpar-method | A class handling parent ion tolerance |
| import | A class referencing an asynchronous execution of MS-GF+ |
| import-method | A class referencing an asynchronous execution of MS-GF+ |
| instrument | Get and set instrument in msgfPar objects |
| instrument-method | Get and set instrument in msgfPar objects |
| instrument<- | Get and set instrument in msgfPar objects |
| instrument<--method | Get and set instrument in msgfPar objects |
| isotopeError | Get and set isotope error in msgfPar objects |
| isotopeError-method | Get and set isotope error in msgfPar objects |
| isotopeError<- | Get and set isotope error in msgfPar objects |
| isotopeError<--method | Get and set isotope error in msgfPar objects |
| length-method | A class to contain parameters used in an MS-GF+ analysis |
| length-method | A class handling charge ranges |
| length-method | A class handling enzyme selection |
| length-method | A class handling Fragmentation types |
| length-method | A class handling instrument types |
| length-method | A class handling isotope errors |
| length-method | A class handling length ranges |
| length-method | A class handling number of matches |
| length-method | A class handling a list of modifications |
| length-method | A class handling cleavage specificity |
| length-method | A class handling protocol choice |
| length-method | A class handling use of target-decoy approach for FDR estimation |
| length-method | A class handling parent ion tolerance |
| lengthRange | Get and set peptide length range in msgfPar objects |
| lengthRange-method | Get and set peptide length range in msgfPar objects |
| lengthRange<- | Get and set peptide length range in msgfPar objects |
| lengthRange<--method | Get and set peptide length range in msgfPar objects |
| matches | Get and set the number of matches in msgfPar objects |
| matches-method | Get and set the number of matches in msgfPar objects |
| matches<- | Get and set the number of matches in msgfPar objects |
| matches<--method | Get and set the number of matches in msgfPar objects |
| mods | Get and set the modifications in msgfPar objects |
| mods-method | Get and set the modifications in msgfPar objects |
| mods<- | Get and set the modifications in msgfPar objects |
| mods<--method | Get and set the modifications in msgfPar objects |
| msgfAsync-class | A class referencing an asynchronous execution of MS-GF+ |
| msgfPar | Constructor for the msgfPar class |
| msgfPar-class | A class to contain parameters used in an MS-GF+ analysis |
| msgfParChargeRange | A class handling charge ranges |
| msgfParChargeRange-class | A class handling charge ranges |
| msgfParEnzyme | A class handling enzyme selection |
| msgfParEnzyme-class | A class handling enzyme selection |
| msgfParFragmentation | A class handling Fragmentation types |
| msgfParFragmentation-class | A class handling Fragmentation types |
| msgfParFromID | Extract parameters from mzIdentML result file |
| msgfParGUI | A simple GUI to create msgfPar objects |
| msgfParInstrument | A class handling instrument types |
| msgfParInstrument-class | A class handling instrument types |
| msgfParIsotopeError | A class handling isotope errors |
| msgfParIsotopeError-class | A class handling isotope errors |
| msgfParLengthRange | A class handling length ranges |
| msgfParLengthRange-class | A class handling length ranges |
| msgfParMatches | A class handling number of matches |
| msgfParMatches-class | A class handling number of matches |
| msgfParModification | A class handling modification characteristics |
| msgfParModification-class | A class handling modification characteristics |
| msgfParModificationList | A class handling a list of modifications |
| msgfParModificationList-class | A class handling a list of modifications |
| msgfParNtt | A class handling cleavage specificity |
| msgfParNtt-class | A class handling cleavage specificity |
| msgfParProtocol | A class handling protocol choice |
| msgfParProtocol-class | A class handling protocol choice |
| msgfParTda | A class handling use of target-decoy approach for FDR estimation |
| msgfParTda-class | A class handling use of target-decoy approach for FDR estimation |
| msgfParTolerance | A class handling parent ion tolerance |
| msgfParTolerance-class | A class handling parent ion tolerance |
| nMod | Get and set the modifications in msgfPar objects |
| nMod-method | Get and set the modifications in msgfPar objects |
| nMod<- | Get and set the modifications in msgfPar objects |
| nMod<--method | Get and set the modifications in msgfPar objects |
| ntt | Get and set cleavage specificity in msgfPar objects |
| ntt-method | Get and set cleavage specificity in msgfPar objects |
| ntt<- | Get and set cleavage specificity in msgfPar objects |
| ntt<--method | Get and set cleavage specificity in msgfPar objects |
| protocol | Get and set protocol in msgfPar objects |
| protocol-method | Get and set protocol in msgfPar objects |
| protocol<- | Get and set protocol in msgfPar objects |
| protocol<--method | Get and set protocol in msgfPar objects |
| runMSGF | Runs MS-GF+ based on the given msgfPar object |
| runMSGF-method | A class to contain parameters used in an MS-GF+ analysis |
| running | A class referencing an asynchronous execution of MS-GF+ |
| running-method | A class referencing an asynchronous execution of MS-GF+ |
| show-method | A class to contain parameters used in an MS-GF+ analysis |
| show-method | A class handling charge ranges |
| show-method | A class handling enzyme selection |
| show-method | A class handling Fragmentation types |
| show-method | A class handling instrument types |
| show-method | A class handling isotope errors |
| show-method | A class handling length ranges |
| show-method | A class handling number of matches |
| show-method | A class handling modification characteristics |
| show-method | A class handling a list of modifications |
| show-method | A class handling cleavage specificity |
| show-method | A class handling protocol choice |
| show-method | A class handling use of target-decoy approach for FDR estimation |
| show-method | A class handling parent ion tolerance |
| tda | Get and set use of target-decoy approach in msgfPar objects |
| tda-method | Get and set use of target-decoy approach in msgfPar objects |
| tda<- | Get and set use of target-decoy approach in msgfPar objects |
| tda<--method | Get and set use of target-decoy approach in msgfPar objects |
| tolerance | Get and set the parent tolerance in msgfPar objects |
| tolerance-method | Get and set the parent tolerance in msgfPar objects |
| tolerance<- | Get and set the parent tolerance in msgfPar objects |
| tolerance<--method | Get and set the parent tolerance in msgfPar objects |
| toleranceRange | Get and set the parent tolerance in msgfPar objects |
| toleranceRange-method | Get and set the parent tolerance in msgfPar objects |
| toleranceRange<- | Get and set the parent tolerance in msgfPar objects |
| toleranceRange<--method | Get and set the parent tolerance in msgfPar objects |
| toleranceUnit | Get and set the parent tolerance in msgfPar objects |
| toleranceUnit-method | Get and set the parent tolerance in msgfPar objects |
| toleranceUnit<- | Get and set the parent tolerance in msgfPar objects |
| toleranceUnit<--method | Get and set the parent tolerance in msgfPar objects |
| [[-method | A class handling a list of modifications |
| [[<--method | A class handling a list of modifications |