Man pages for lgatto/RpepXML
R interface to the pepXML standard

as.matrix.MSMSpepXMLTransforms an 'MSMSpepXML' object in a simplified matrix.
assumedCharge-methodsAccessor methods of the 'assumedCharge' slot
filterHits-methodsMethod to filter hits based on their rand and ion score.
hitRank-methodsAccessor methods of the 'hitRank' slot
ionScore-methodsAccessor methods of the ion score in the 'scores' slot
modifications-methodsAccessor methods of the 'modifications' slot
MSMSpepXML-classClass to contain MSMS peptide identification data.
nProteins-methodsReturns the number of identified proteins.
nSearchHits-methodsReturns the number of search hits.
nSearchResults-methodsReturns the number of search results.
nSpectrumQueries-methodsReturns the numbre of search queries.
parseMSMSpepXMLRead a pepXML file into R
pepFile-methodsReturn returns the pepXML file name.
pepSequence-methodsReturns the sequence(s) of an identified peptide.
precNeutralMass-methodsReturns the precursor's neutral mass.
proteins-methodsReturns the proteins associated with identifies peptides.
proteinSummaryReturn a table of identified proteins.
queryIndex-methodsReturns the spectrum query index.
RpepXML-packageR interface to the pepXML standard
sampleEnzyme-methodsReturns the sample enzyme.
scores-methodsReturns the peptide search scores.
searchDatabase-methodsReturns the search database name.
searchEngine-methodsReturns the name of the search engine.
SearchHit-classClass to contain individual search hit identification data.
searchHits-methodsReturns the search hit(s) of a search result.
searchId-methodsReturns the id of the search result.
SearchResult-classClass to contain individual search result data.
searchResults-methodsReturns the search result(s) of a spectrum query.
spectrumId-methodsReturns the id of a spectrum query.
spectrumQueries-methodsReturns the spectrum query(ies).
SpectrumQuery-classClass to contain individual spectrum query identification...
startScan-methodsAccessor of the 'startScan' and 'endScan' slots
lgatto/RpepXML documentation built on May 21, 2017, 12:38 p.m.