| 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 |