R: An interface between R and MS-GF+

# An interface between R and MS-GF+

## Documentation for package ‘MSGFplus’ version 1.28.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

C D E F G I L M N P R S T misc

MSGFplus-package | An interface between R and MS-GF+

## -- C --

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

## -- D --

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

## -- E --

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

## -- F --

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

## -- G --

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

## -- I --

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

## -- L --

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

## -- M --

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
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

## -- N --

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

## -- P --

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

## -- R --

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+

## -- S --

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

## -- T --

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

## -- misc --

[[-method | A class handling a list of modifications
[[<--method | A class handling a list of modifications