An interface between R and MS-GF+


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Documentation for package ‘MSGFplus’ version 1.4.0

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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+

-- 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
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

-- 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