rTANDEM: Interfaces the tandem protein identification algorithm in R
Version 1.16.0

This package interfaces the tandem protein identification algorithm in R. Identification can be launched in the X!Tandem style, by using as sole parameter the path to a parameter file. But rTANDEM aslo provides extended syntax and functions to streamline launching analyses, as well as function to convert results, parameters and taxonomy to/from R. A related package, shinyTANDEM, provides visualization interface for result objects.

AuthorFrederic Fournier <frederic.fournier@crchuq.ulaval.ca>, Charles Joly Beauparlant <charles.joly-beauparlant@crchul.ulaval.ca>, Rene Paradis <rene.paradis@genome.ulaval.ca>, Arnaud Droit <arnaud.droit@crchuq.ulaval.ca>
Bioconductor views MassSpectrometry Proteomics
Date of publicationNone
MaintainerFrederic Fournier <frederic.fournier@crchuq.ulaval.ca>
LicenseArtistic-1.0 | file LICENSE
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rTANDEM")

Getting started

Package overview

Popular man pages

accessors: Extract information from rTANDEM result object
converters: Converts X!Tandem xml files to R objects and vice versa
parameters: Creates and manipulates parameter objects for rTANDEM
rTANDEM-package: An R encapsulation of X!TANDEM ('Jackhammer' release,...
rTResult-class: Class "rTResult" and "rTResult_s"
tandem: Calls X!TANDEM ('Jackhammer' release, 2013.06.15) from R...
visualizers: Plot spectrum from a rTResult object
See all...

All man pages Function index File listing

Man pages

accessors: Extract information from rTANDEM result object
converters: Converts X!Tandem xml files to R objects and vice versa
parameters: Creates and manipulates parameter objects for rTANDEM
rTANDEM-package: An R encapsulation of X!TANDEM ('Jackhammer' release,...
rTResult-class: Class "rTResult" and "rTResult_s"
tandem: Calls X!TANDEM ('Jackhammer' release, 2013.06.15) from R...
visualizers: Plot spectrum from a rTResult object

Functions

AddTaxon Man page
GetDegeneracy Man page Source code
GetParamFromXML Man page Source code
GetPeptides Man page Source code
GetProteins Man page Source code
GetResultsFromXML Man page Source code
GetTaxoFromXML Man page Source code
SetParamDefault Man page
SetParamIonTrap Man page
SetParamOrbitrap Man page
SetParamPTMTreeSearch Man page
SetParamQuadTof05da Man page
SetParamQuadTof100ppm Man page
SetParamValue Man page
WriteParamToXML Man page Source code
WriteTaxoToXML Man page Source code
addTaxon Man page Source code
checkParam Source code
getDegeneracy Man page
getParamFromXML Man page
getPeptides Man page
getProteins Man page
getResultsFromXML Man page
getTaxoFromXML Man page
ms2.plot Man page Source code
print.rTParam Man page Source code
rTANDEM Man page
rTANDEM-package Man page
rTParam Man page Source code
rTResult-class Man page
rTResult_s-class Man page
rTTaxo Man page Source code
rtandem Man page Source code
setParamDefault Man page Source code
setParamIonTrap Man page Source code
setParamOrbitrap Man page Source code
setParamPTMTreeSearch Man page Source code
setParamQuadTof05da Man page Source code
setParamQuadTof100ppm Man page Source code
setParamValue Man page Source code
tandem Man page Source code
writeParamToXML Man page
writeTaxoToXML Man page

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/accessors.R
R/converters.R
R/parameters.R
R/rTANDEM.R
R/results.R
R/visualizers.R
README
build
build/vignette.rds
inst
inst/doc
inst/doc/rTANDEM.R
inst/doc/rTANDEM.Rnw
inst/doc/rTANDEM.pdf
inst/extdata
inst/extdata/default_input.xml
inst/extdata/fasta
inst/extdata/fasta/scd.fasta.pro
inst/extdata/input.xml
inst/extdata/ptmlist.txt
inst/extdata/result.xml
inst/extdata/tandem-input-style.xsl
inst/extdata/tandem-style.css
inst/extdata/tandem-style.xsl
inst/extdata/taxonomy.xml
inst/extdata/test_spectra.mgf
man
man/accessors.Rd
man/converters.Rd
man/parameters.Rd
man/rTANDEM-package.Rd
man/rTResult-class.Rd
man/tandem.Rd
man/visualizers.Rd
src
src/Makevars
src/Makevars.in
src/Makevars.win
src/PTMTreeSearch.cpp
src/PTMTreeSearch.h
src/PTMTreeSearchScore.cpp
src/PTMTreeSearchScore.h
src/base64.cpp
src/base64.h
src/dataLoader.cpp
src/dataLoader.h
src/expat.h
src/expat_external.h
src/expat_external_old.h
src/expat_old.h
src/loadmspectrum.cpp
src/loadmspectrum.h
src/masscalc.cpp
src/masscalc.h
src/mbiomlreport.cpp
src/mbiomlreport.h
src/mcleave.h
src/mdomains.h
src/mhistogram.h
src/mmotif.h
src/mpam.cpp
src/mpam.h
src/mplugin.cpp
src/mplugin.h
src/mpmods.cpp
src/mpmods.h
src/mprocess.cpp
src/mprocess.h
src/mrefine.cpp
src/mrefine.h
src/mreport.cpp
src/mreport.h
src/mscore.cpp
src/mscore.h
src/mscore_hrk.cpp
src/mscore_hrk.h
src/mscore_k.cpp
src/mscore_k.h
src/mscore_tandem.cpp
src/mscore_tandem.h
src/mscorepam.h
src/mscorestate.h
src/msemistate.h
src/msequence.h
src/msequencecollection.cpp
src/msequencecollection.h
src/msequenceserver.cpp
src/msequenceserver.h
src/msequtilities.cpp
src/msequtilities.h
src/mspectrum.h
src/mspectrumcondition.cpp
src/mspectrumcondition.h
src/mtermmods.cpp
src/mtermmods.h
src/mxxcleavage.cpp
src/mxxcleavage.h
src/resource.h
src/saxbiomlhandler.cpp
src/saxbiomlhandler.h
src/saxgamlhandler.cpp
src/saxgamlhandler.h
src/saxhandler.cpp
src/saxhandler.h
src/saxmodhandler.cpp
src/saxmodhandler.h
src/saxmzdatahandler.cpp
src/saxmzdatahandler.h
src/saxmzmlhandler.cpp
src/saxmzmlhandler.h
src/saxmzxmlhandler.cpp
src/saxmzxmlhandler.h
src/saxsaphandler.cpp
src/saxsaphandler.h
src/saxtandeminputhandler.cpp
src/saxtandeminputhandler.h
src/saxtaxhandler.cpp
src/saxtaxhandler.h
src/stack_ptmtreesearch.h
src/stdafx.cpp
src/stdafx.h
src/tandem.cpp
src/tandem.h
src/xmlparameter.cpp
src/xmlparameter.h
src/xmltaxonomy.cpp
src/xmltaxonomy.h
vignettes
vignettes/rTANDEM.Rnw
rTANDEM documentation built on May 20, 2017, 10:50 p.m.

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