API for MSGFplus
An interface between R and MS-GF+

Global functions
.javaExecutable	Source code
.onLoad	Source code
MSGFplus-package	Man page
Sys.which2	Source code
[[,msgfParModificationList,numeric,missing-method	Man page
[[<-,msgfParModificationList,numeric,missing,msgfParModification	Man page
chargeRange	Man page
chargeRange,msgfPar-method	Man page
chargeRange<-	Man page
chargeRange<-,msgfPar,msgfParChargeRange-method	Man page
chargeRange<-,msgfPar,numeric-method	Man page
createFileCall	Source code
db	Man page
db,msgfPar-method	Man page
db<-	Man page
db<-,msgfPar,character-method	Man page
enzyme	Man page
enzyme,msgfPar-method	Man page
enzyme<-	Man page
enzyme<-,msgfPar,character-method	Man page
enzyme<-,msgfPar,msgfParEnzyme-method	Man page
enzyme<-,msgfPar,numeric-method	Man page
enzymeLookup	Source code
finished	Man page
finished,msgfAsync-method	Man page
fragmentation	Man page
fragmentation,msgfPar-method	Man page
fragmentation<-	Man page
fragmentation<-,msgfPar,character-method	Man page
fragmentation<-,msgfPar,msgfParFragmentation-method	Man page
fragmentation<-,msgfPar,numeric-method	Man page
fragmentationLookup	Source code
getMSGFpar	Man page
getMSGFpar,msgfPar-method	Man page
getMSGFpar,msgfParChargeRange-method	Man page
getMSGFpar,msgfParEnzyme-method	Man page
getMSGFpar,msgfParFragmentation-method	Man page
getMSGFpar,msgfParInstrument-method	Man page
getMSGFpar,msgfParIsotopeError-method	Man page
getMSGFpar,msgfParLengthRange-method	Man page
getMSGFpar,msgfParMatches-method	Man page
getMSGFpar,msgfParModification-method	Man page
getMSGFpar,msgfParModificationList-method	Man page
getMSGFpar,msgfParNtt-method	Man page
getMSGFpar,msgfParProtocol-method	Man page
getMSGFpar,msgfParTda-method	Man page
getMSGFpar,msgfParTolerance-method	Man page
getMSGFplus	Source code
import	Man page
import,msgfAsync-method	Man page
instrument	Man page
instrument,msgfPar-method	Man page
instrument<-	Man page
instrument<-,msgfPar,character-method	Man page
instrument<-,msgfPar,msgfParInstrument-method	Man page
instrument<-,msgfPar,numeric-method	Man page
instrumentLookup	Source code
isotopeError	Man page
isotopeError,msgfPar-method	Man page
isotopeError<-	Man page
isotopeError<-,msgfPar,msgfParIsotopeError-method	Man page
isotopeError<-,msgfPar,numeric-method	Man page
length,msgfPar-method	Man page
length,msgfParChargeRange-method	Man page
length,msgfParEnzyme-method	Man page
length,msgfParFragmentation-method	Man page
length,msgfParInstrument-method	Man page
length,msgfParIsotopeError-method	Man page
length,msgfParLengthRange-method	Man page
length,msgfParMatches-method	Man page
length,msgfParModificationList-method	Man page
length,msgfParNtt-method	Man page
length,msgfParProtocol-method	Man page
length,msgfParTda-method	Man page
length,msgfParTolerance-method	Man page
lengthRange	Man page
lengthRange,msgfPar-method	Man page
lengthRange<-	Man page
lengthRange<-,msgfPar,msgfParLengthRange-method	Man page
lengthRange<-,msgfPar,numeric-method	Man page
matches	Man page
matches,msgfPar-method	Man page
matches<-	Man page
matches<-,msgfPar,msgfParMatches-method	Man page
matches<-,msgfPar,numeric-method	Man page
mods	Man page
mods,msgfPar-method	Man page
mods<-	Man page
mods<-,msgfPar,msgfParModificationList-method	Man page
msgfAsync-class	Man page
msgfPar	Man page Source code
msgfPar-class	Man page
msgfParChargeRange	Man page Source code
msgfParChargeRange-class	Man page
msgfParEnzyme	Man page Source code
msgfParEnzyme-class	Man page
msgfParFragmentation	Man page Source code
msgfParFragmentation-class	Man page
msgfParFromID	Man page Source code
msgfParInstrument	Man page Source code
msgfParInstrument-class	Man page
msgfParIsotopeError	Man page Source code
msgfParIsotopeError-class	Man page
msgfParLengthRange	Man page Source code
msgfParLengthRange-class	Man page
msgfParMatches	Man page Source code
msgfParMatches-class	Man page
msgfParModification	Man page Source code
msgfParModification-class	Man page
msgfParModificationList	Man page Source code
msgfParModificationList-class	Man page
msgfParNtt	Man page Source code
msgfParNtt-class	Man page
msgfParProtocol	Man page Source code
msgfParProtocol-class	Man page
msgfParTda	Man page Source code
msgfParTda-class	Man page
msgfParTolerance	Man page Source code
msgfParTolerance-class	Man page
nMod	Man page
nMod,msgfPar-method	Man page
nMod<-	Man page
nMod<-,msgfPar,numeric-method	Man page
ntt	Man page
ntt,msgfPar-method	Man page
ntt<-	Man page
ntt<-,msgfPar,msgfParNtt-method	Man page
ntt<-,msgfPar,numeric-method	Man page
protocol	Man page
protocol,msgfPar-method	Man page
protocol<-	Man page
protocol<-,msgfPar,character-method	Man page
protocol<-,msgfPar,msgfParProtocol-method	Man page
protocol<-,msgfPar,numeric-method	Man page
protocolLookup	Source code
runMSGF	Man page
runMSGF,msgfPar-method	Man page
running	Man page
running,msgfAsync-method	Man page
show,msgfPar-method	Man page
show,msgfParChargeRange-method	Man page
show,msgfParEnzyme-method	Man page
show,msgfParFragmentation-method	Man page
show,msgfParInstrument-method	Man page
show,msgfParIsotopeError-method	Man page
show,msgfParLengthRange-method	Man page
show,msgfParMatches-method	Man page
show,msgfParModification-method	Man page
show,msgfParModificationList-method	Man page
show,msgfParNtt-method	Man page
show,msgfParProtocol-method	Man page
show,msgfParTda-method	Man page
show,msgfParTolerance-method	Man page
tda	Man page
tda,msgfPar-method	Man page
tda<-	Man page
tda<-,msgfPar,logical-method	Man page
tda<-,msgfPar,msgfParTda-method	Man page
tolerance	Man page
tolerance,msgfPar-method	Man page
tolerance<-	Man page
tolerance<-,msgfPar,character-method	Man page
tolerance<-,msgfPar,msgfParTolerance-method	Man page
toleranceRange	Man page
toleranceRange,msgfPar-method	Man page
toleranceRange<-	Man page
toleranceRange<-,msgfPar,numeric-method	Man page
toleranceUnit	Man page
toleranceUnit,msgfPar-method	Man page
toleranceUnit<-	Man page
toleranceUnit<-,msgfPar,character-method	Man page