Man pages for RpepXML
R interface to the pepXML standard

as.matrix.MSMSpepXML	Transforms an 'MSMSpepXML' object in a simplified matrix.
assumedCharge-methods	Accessor methods of the 'assumedCharge' slot
filterHits-methods	Method to filter hits based on their rand and ion score.
hitRank-methods	Accessor methods of the 'hitRank' slot
ionScore-methods	Accessor methods of the ion score in the 'scores' slot
modifications-methods	Accessor methods of the 'modifications' slot
MSMSpepXML-class	Class to contain MSMS peptide identification data.
nProteins-methods	Returns the number of identified proteins.
nSearchHits-methods	Returns the number of search hits.
nSearchResults-methods	Returns the number of search results.
nSpectrumQueries-methods	Returns the numbre of search queries.
parseMSMSpepXML	Read a pepXML file into R
pepFile-methods	Return returns the pepXML file name.
pepSequence-methods	Returns the sequence(s) of an identified peptide.
precNeutralMass-methods	Returns the precursor's neutral mass.
proteins-methods	Returns the proteins associated with identifies peptides.
proteinSummary	Return a table of identified proteins.
queryIndex-methods	Returns the spectrum query index.
RpepXML-package	R interface to the pepXML standard
sampleEnzyme-methods	Returns the sample enzyme.
scores-methods	Returns the peptide search scores.
searchDatabase-methods	Returns the search database name.
searchEngine-methods	Returns the name of the search engine.
SearchHit-class	Class to contain individual search hit identification data.
searchHits-methods	Returns the search hit(s) of a search result.
searchId-methods	Returns the id of the search result.
SearchResult-class	Class to contain individual search result data.
searchResults-methods	Returns the search result(s) of a spectrum query.
spectrumId-methods	Returns the id of a spectrum query.
spectrumQueries-methods	Returns the spectrum query(ies).
SpectrumQuery-class	Class to contain individual spectrum query identification...
startScan-methods	Accessor of the 'startScan' and 'endScan' slots