CHANGES IN VERSION 1.3.9 ------------------------ o Capitalisation aliases added for most functions. o The rtandem function now has an 'output.path' argument. BUG FIXES o Changed default parameters to prevent the risk of not generating output files. o Fixed a bug with 'rtandem()' where the function would not take a complex rTTAXO object as argument. CHANGES IN VERSION 1.3.8 ------------------------ BUG FIXES o Fixed a memory leak associated with PTMTreeSearch. o Removed an unwanted side-effect from the function GetPeptides(). CHANGES IN VERSION 1.3.7 ------------------------ NEW FEATURES o rTANDEM now includes the PTMTreeSearch scoring algorithm. o New function to set default values for PTMTreeSearch algorithm. CHANGES IN VERSION 1.3.5 ------------------------ NEW FEATURES o New rTResult_s class support saving spectra. o New function 'ms2.plot' to visualize spectra. CHANGES IN VERSION 1.3.4 ------------------------ NEW FEATURES o rTANDEM now supports TPP's hrk-score function. BUG FIXES o Fixed a bug with k-score function. CHANGES IN VERSION 1.3.3 ------------------------ NEW FEATURES o Functions have been implemented to create and manipulate parameter objects (S3 class rTParam). Those functions give default values for instrument-specific parameters for some types of mass spectrometer as well as default values for general parameters. CHANGES IN VERSION 1.3.2 ------------------------ NEW FEATURES o rTANDEM now supports the k-score function. It can be used by setting the parameter 'scoring, algorithm' to "k-score". CHANGES IN VERSION 1.1.6 ------------------------ NEW FEATURES o rTANDEM is now based on x!tandem version 13-09-01 'sledgehammer' CHANGES IN VERSION 1.1.5 ------------------------ BUG FIXES o Fixed a memory management problen in Cpp NEW FEATURES o More parameters are supported. CHANGES IN VERSION 1.1.4 ------------------------ NEW FEATURES o rTANDEM is now based on x!tandem version 13-06-15 'jackhammer' BUG FIXES o Corrected a bug that prevented the use of multi-threading o Corrected a bug that could affect results when multiple fasta files are assigned to a same taxon.