RpepXML: R interface to the pepXML standard

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R package to import and manipulate pepXML data.

Author
Laurent Gatto
Date of publication
None
Maintainer
Laurent Gatto <lg390@cam.ac.uk>
License
Artistic-2.0
Version
0.3.3

View on R-Forge

Man pages

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

Files in this package

RpepXML
RpepXML/R
RpepXML/R/SearchResult-class.R
RpepXML/R/functions-parser.R
RpepXML/R/SpectrumQuery-class.R
RpepXML/R/MSMSpepXML-class.R
RpepXML/R/AllGenerics.R
RpepXML/R/SearchHit-class.R
RpepXML/NAMESPACE
RpepXML/inst
RpepXML/inst/doc
RpepXML/inst/doc/RpepXML.pdf
RpepXML/inst/doc/RpepXML.Rnw
RpepXML/inst/doc/Z.cls
RpepXML/inst/extdata
RpepXML/inst/extdata/tinySearch.csv
RpepXML/inst/extdata/tinySearch.pepXML
RpepXML/TODO
RpepXML/DESCRIPTION
RpepXML/man
RpepXML/man/hitRank-methods.Rd
RpepXML/man/sampleEnzyme-methods.Rd
RpepXML/man/nProteins-methods.Rd
RpepXML/man/precNeutralMass-methods.Rd
RpepXML/man/proteins-methods.Rd
RpepXML/man/SearchHit-class.Rd
RpepXML/man/searchEngine-methods.Rd
RpepXML/man/pepFile-methods.Rd
RpepXML/man/as.matrix.MSMSpepXML.Rd
RpepXML/man/parseMSMSpepXML.Rd
RpepXML/man/spectrumQueries-methods.Rd
RpepXML/man/SearchResult-class.Rd
RpepXML/man/nSearchHits-methods.Rd
RpepXML/man/searchHits-methods.Rd
RpepXML/man/ionScore-methods.Rd
RpepXML/man/filterHits-methods.Rd
RpepXML/man/proteinSummary.Rd
RpepXML/man/MSMSpepXML-class.Rd
RpepXML/man/searchResults-methods.Rd
RpepXML/man/RpepXML-package.Rd
RpepXML/man/searchDatabase-methods.Rd
RpepXML/man/modifications-methods.Rd
RpepXML/man/startScan-methods.Rd
RpepXML/man/queryIndex-methods.Rd
RpepXML/man/searchId-methods.Rd
RpepXML/man/nSpectrumQueries-methods.Rd
RpepXML/man/spectrumId-methods.Rd
RpepXML/man/pepSequence-methods.Rd
RpepXML/man/assumedCharge-methods.Rd
RpepXML/man/scores-methods.Rd
RpepXML/man/SpectrumQuery-class.Rd
RpepXML/man/nSearchResults-methods.Rd
RpepXML/NEWS