API for RpepXML
R interface to the pepXML standard

Global functions
MSMSpepXML-class	Man page
RpepXML	Man page
RpepXML-package	Man page
SearchHit-class	Man page
SearchResult-class	Man page
SpectrumQuery-class	Man page
[,MSMSpepXML-method	Man page
[,SearchResult-method	Man page
[,SpectrumQuery-method	Man page
as.matrix.MSMSpepXML	Man page Source code
assumedCharge	Man page
assumedCharge,MSMSpepXML-method	Man page
assumedCharge,SpectrumQuery-method	Man page
assumedCharge-methods	Man page
assumedCharge<-	Man page
assumedCharge<-,SpectrumQuery,ANY-method	Man page
assumedCharge<-,SpectrumQuery,numeric-method	Man page
endScan	Man page
endScan,SpectrumQuery-method	Man page
endScan-methods	Man page
endScan<-	Man page
endScan<-,SpectrumQuery,ANY-method	Man page
endScan<-,SpectrumQuery,integer-method	Man page
filterHits	Man page
filterHits,MSMSpepXML-method	Man page Man page
filterHits,SearchHit-method	Man page
filterHits,SearchResult-method	Man page
filterHits,SpectrumQuery-method	Man page
filterHits-methods	Man page
getSearchHits	Source code
getSearchHits.old	Source code
getSearchResults	Source code
getSearchResults.old	Source code
hitRank	Man page
hitRank,SearchHit-method	Man page
hitRank,SearchResult-method	Man page
hitRank-methods	Man page
hitRank<-	Man page
hitRank<-,SearchHit,ANY-method	Man page
hitRank<-,SearchHit,integer-method	Man page
ionScore	Man page
ionScore,SearchHit-method	Man page
ionScore-methods	Man page
modifications	Man page
modifications,SearchHit-method	Man page
modifications-methods	Man page
modifications<-	Man page
modifications<-,SearchHit,ANY-method	Man page
modifications<-,SearchHit,data.frame-method	Man page
nProteins	Man page
nProteins,MSMSpepXML-method	Man page
nProteins,SearchHit-method	Man page
nProteins,SearchResult-method	Man page
nProteins,SpectrumQuery-method	Man page
nProteins-methods	Man page
nSearchHits	Man page
nSearchHits,MSMSpepXML-method	Man page
nSearchHits,SearchResult-method	Man page
nSearchHits,SpectrumQuery-method	Man page
nSearchHits-methods	Man page
nSearchResults	Man page
nSearchResults,MSMSpepXML-method	Man page
nSearchResults,SpectrumQuery-method	Man page
nSearchResults-methods	Man page
nSpectrumQueries	Man page
nSpectrumQueries,MSMSpepXML-method	Man page
nSpectrumQueries-methods	Man page
parseMSMSpepXML	Man page Source code
parseMSMSpepXMLfile.old	Source code
pepFile	Man page
pepFile,MSMSpepXML-method	Man page
pepFile-methods	Man page
pepFile<-	Man page
pepFile<-,MSMSpepXML,ANY-method	Man page
pepFile<-,MSMSpepXML,character-method	Man page
pepSequence	Man page
pepSequence,MSMSpepXML-method	Man page
pepSequence,SearchHit-method	Man page
pepSequence,SearchResult-method	Man page
pepSequence,SpectrumQuery-method	Man page
pepSequence-methods	Man page
pepSequence<-	Man page
pepSequence<-,SearchHit,ANY-method	Man page
pepSequence<-,SearchHit,character-method	Man page
precNeutralMass	Man page
precNeutralMass,MSMSpepXML-method	Man page
precNeutralMass,SpectrumQuery-method	Man page
precNeutralMass-methods	Man page
precNeutralMass<-	Man page
precNeutralMass<-,SpectrumQuery,ANY-method	Man page
precNeutralMass<-,SpectrumQuery,numeric-method	Man page
proteinSummary	Man page Source code
proteins	Man page
proteins,MSMSpepXML-method	Man page
proteins,SearchHit-method	Man page
proteins,SearchResult-method	Man page
proteins,SpectrumQuery-method	Man page
proteins-methods	Man page
proteins<-	Man page
proteins<-,SearchHit,ANY-method	Man page
proteins<-,SearchHit,character-method	Man page
queryIndex	Man page
queryIndex,SpectrumQuery-method	Man page
queryIndex-methods	Man page
queryIndex<-	Man page
queryIndex<-,SpectrumQuery,ANY-method	Man page
queryIndex<-,SpectrumQuery,integer-method	Man page
sampleEnzyme	Man page
sampleEnzyme,MSMSpepXML-method	Man page
sampleEnzyme-methods	Man page
sampleEnzyme<-	Man page
sampleEnzyme<-,MSMSpepXML,ANY-method	Man page
sampleEnzyme<-,MSMSpepXML,character-method	Man page
scores	Man page
scores,MSMSpepXML-method	Man page
scores,SearchHit-method	Man page
scores,SearchResult-method	Man page
scores,SpectrumQuery-method	Man page
scores-methods	Man page
scores<-	Man page
scores<-,SearchHit,ANY-method	Man page
scores<-,SearchHit,numeric-method	Man page
searchDatabase	Man page
searchDatabase,MSMSpepXML-method	Man page
searchDatabase-methods	Man page
searchDatabase<-	Man page
searchDatabase<-,MSMSpepXML,ANY-method	Man page
searchDatabase<-,MSMSpepXML,character-method	Man page
searchEngine	Man page
searchEngine,MSMSpepXML-method	Man page
searchEngine-methods	Man page
searchEngine<-	Man page
searchEngine<-,MSMSpepXML,ANY-method	Man page
searchEngine<-,MSMSpepXML,character-method	Man page
searchHits	Man page
searchHits,SearchResult-method	Man page
searchHits-methods	Man page
searchHits<-	Man page
searchHits<-,SearchResult,ANY-method	Man page
searchHits<-,SearchResult,list-method	Man page
searchId	Man page
searchId,SearchResult-method	Man page
searchId-methods	Man page
searchId<-	Man page
searchId<-,SearchResult,ANY-method	Man page
searchId<-,SearchResult,integer-method	Man page
searchResults	Man page
searchResults,SpectrumQuery-method	Man page
searchResults-methods	Man page
searchResults<-	Man page
searchResults<-,SpectrumQuery,ANY-method	Man page
searchResults<-,SpectrumQuery,list-method	Man page
show,MSMSpepXML-method	Man page
show,SearchHit-method	Man page
show,SearchResult-method	Man page
show,SpectrumQuery-method	Man page
spectrumId	Man page
spectrumId,SpectrumQuery-method	Man page
spectrumId-methods	Man page
spectrumId<-	Man page
spectrumId<-,SpectrumQuery,ANY-method	Man page
spectrumId<-,SpectrumQuery,character-method	Man page
spectrumQueries	Man page
spectrumQueries,MSMSpepXML-method	Man page
spectrumQueries-methods	Man page
spectrumQueries<-	Man page
spectrumQueries<-,MSMSpepXML,ANY-method	Man page
spectrumQueries<-,MSMSpepXML,list-method	Man page
startScan	Man page
startScan,SpectrumQuery-method	Man page
startScan-methods	Man page
startScan<-	Man page
startScan<-,SpectrumQuery,ANY-method	Man page
startScan<-,SpectrumQuery,integer-method	Man page