Interfaces the tandem protein identification algorithm in R


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Documentation for package ‘rTANDEM’ version 1.8.0

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rTANDEM-package An R encapsulation of X!TANDEM ('Jackhammer' release, 2013.06.15)
AddTaxon Creates and manipulates parameter objects for rTANDEM
addTaxon Creates and manipulates parameter objects for rTANDEM
GetDegeneracy Extract information from rTANDEM result object
getDegeneracy Extract information from rTANDEM result object
GetParamFromXML Converts X!Tandem xml files to R objects and vice versa
getParamFromXML Converts X!Tandem xml files to R objects and vice versa
GetPeptides Extract information from rTANDEM result object
getPeptides Extract information from rTANDEM result object
GetProteins Extract information from rTANDEM result object
getProteins Extract information from rTANDEM result object
GetResultsFromXML Converts X!Tandem xml files to R objects and vice versa
getResultsFromXML Converts X!Tandem xml files to R objects and vice versa
GetTaxoFromXML Converts X!Tandem xml files to R objects and vice versa
getTaxoFromXML Converts X!Tandem xml files to R objects and vice versa
ms2.plot Plot spectrum from a rTResult object
print.rTParam Creates and manipulates parameter objects for rTANDEM
rTANDEM Calls X!TANDEM ('Jackhammer' release, 2013.06.15) from R objects or xml files
rtandem Calls X!TANDEM ('Jackhammer' release, 2013.06.15) from R objects or xml files
rTParam Creates and manipulates parameter objects for rTANDEM
rTResult-class Class "rTResult" and "rTResult_s"
rTResult_s-class Class "rTResult" and "rTResult_s"
rTTaxo Creates and manipulates parameter objects for rTANDEM
SetParamDefault Creates and manipulates parameter objects for rTANDEM
setParamDefault Creates and manipulates parameter objects for rTANDEM
SetParamIonTrap Creates and manipulates parameter objects for rTANDEM
setParamIonTrap Creates and manipulates parameter objects for rTANDEM
SetParamOrbitrap Creates and manipulates parameter objects for rTANDEM
setParamOrbitrap Creates and manipulates parameter objects for rTANDEM
SetParamPTMTreeSearch Creates and manipulates parameter objects for rTANDEM
setParamPTMTreeSearch Creates and manipulates parameter objects for rTANDEM
SetParamQuadTof05da Creates and manipulates parameter objects for rTANDEM
setParamQuadTof05da Creates and manipulates parameter objects for rTANDEM
SetParamQuadTof100ppm Creates and manipulates parameter objects for rTANDEM
setParamQuadTof100ppm Creates and manipulates parameter objects for rTANDEM
SetParamValue Creates and manipulates parameter objects for rTANDEM
setParamValue Creates and manipulates parameter objects for rTANDEM
tandem Calls X!TANDEM ('Jackhammer' release, 2013.06.15) from R objects or xml files
WriteParamToXML Converts X!Tandem xml files to R objects and vice versa
writeParamToXML Converts X!Tandem xml files to R objects and vice versa
WriteTaxoToXML Converts X!Tandem xml files to R objects and vice versa
writeTaxoToXML Converts X!Tandem xml files to R objects and vice versa