RpepXML: R interface to the pepXML standard

R package to import and manipulate pepXML data.

AuthorLaurent Gatto
Date of publicationNone
MaintainerLaurent Gatto <lg390@cam.ac.uk>
LicenseArtistic-2.0
Version0.3.3

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

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