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

Functions

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.