# Interfaces the tandem protein identification algorithm in R

## Documentation for package ‘rTANDEM’ version 1.22.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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