MSGFplus-package        An interface between R and MS-GF+
chargeRange             Get and set the charge range in msgfPar objects
db                      Get and set database in msgfPar objects
enzyme                  Get and set enzyme in msgfPar objects
fragmentation           Get and set fragmentation in msgfPar objects
getMSGFpar              Get a string representation of an
                        msgfPar-related object
instrument              Get and set instrument in msgfPar objects
isotopeError            Get and set isotope error in msgfPar objects
lengthRange             Get and set peptide length range in msgfPar
                        objects
matches                 Get and set the number of matches in msgfPar
                        objects
mods                    Get and set the modifications in msgfPar
                        objects
msgfPar                 Constructor for the msgfPar class
msgfPar-class           A class to contain parameters used in an MS-GF+
                        analysis
msgfParChargeRange-class
                        A class handling charge ranges
msgfParEnzyme-class     A class handling enzyme selection
msgfParFragmentation-class
                        A class handling Fragmentation types
msgfParFromID           Extract parameters from mzIdentML result file
msgfParInstrument-class
                        A class handling instrument types
msgfParIsotopeError-class
                        A class handling isotope errors
msgfParLengthRange-class
                        A class handling length ranges
msgfParMatches-class    A class handling number of matches
msgfParModification-class
                        A class handling modification characteristics
msgfParModificationList-class
                        A class handling a list of modifications
msgfParNtt-class        A class handling cleavage specificity
msgfParProtocol-class   A class handling protocol choice
msgfParTda-class        A class handling use of target-decoy approach
                        for FDR estimation
msgfParTolerance-class
                        A class handling parent ion tolerance
ntt                     Get and set cleavage specificity in msgfPar
                        objects
protocol                Get and set protocol in msgfPar objects
runMSGF                 Runs MS-GF+ based on the given msgfPar object
running                 A class referencing an asynchronous execution
                        of MS-GF+
tda                     Get and set use of target-decoy approach in
                        msgfPar objects
tolerance               Get and set the parent tolerance in msgfPar
                        objects
