CHANGES IN VERSION 1.5.10-13 ------------------------- USER UNVISIBLE CHANGES o added specLSet class support for cdsw methode o changed Rmd5 vignette style o added cdsw test case o intro new vignette for cdsw method CHANGES IN VERSION 1.5.9 ------------------------- USER UNVISIBLE CHANGES o added test case for read.biliospec CHANGES IN VERSION 1.5.5 - 1.5.8 ------------------------- USER VISIBLE CHANGES o added RT prediction vignette file CHANGES IN VERSION 1.5.4 ------------------------- USER UNVISIBLE CHANGES o changed NAMESPACES and read.bibliospec docu to avoid warnings in 3.3 check CHANGES IN VERSION 1.5.3 ------------------------- USER UNVISIBLE CHANGES o added sqlite files for peptideStd RData CHANGES IN VERSION 1.5.2 ------------------------- USER UNVISIBLE CHANGES o find all signals having two or more in-silico fragment ions. o keep only the nearest fragment ion; if there are more take the first in line CHANGES IN VERSION 1.3.7 ------------------------- USER UNVISIBLE CHANGES o getProteinPeptideTable - added CHANGES IN VERSION 1.3.5 ------------------------- USER UNVISIBLE CHANGES o read.bibliospec - bugfixes CHANGES IN VERSION 1.3.4 ------------------------- USER VISIBLE CHANGES o added Witold Wolski as maintainer USER UNVISIBLE CHANGES o read.bibliospec - replaced old code (for loop) by using mcmapply o added time meassurements to read.bibliospec CHANGES IN VERSION 1.3.3 ------------------------- USER VISIBLE CHANGES o plot::specLSet draws alpha circles iff plot(..., art=TRUE) USER UNVISIBLE CHANGES o .mascot2psmSet buxfix o renamed column name in spectronaut outpu from irt to irt_or_rt CHANGES IN VERSION 1.3.2 ------------------------- USER VISIBLE CHANGES o added ssrc (Sequence Specific Retention Calculator) function o added a CITATION file CHANGES IN VERSION 1.3.1 ------------------------- USER VISIBLE CHANGES o added fucntion cdsw USER UNVISIBLE CHANGES o modified unit test for genSwathIonLib CHANGES IN VERSION 1.1.17 ------------------------- USER UNVISIBLE CHANGES o removed file argument in genSwathIonLib function CHANGES IN VERSION 1.1.16 ------------------------- USER UNVISIBLE CHANGES o added unit test for genSwathIonLib CHANGES IN VERSION 1.1.15 ------------------------- USER UNVISIBLE CHANGES o added circle plots to specLSet plot method o added breaks argument in genSwathIonLib methode CHANGES IN VERSION 1.1.14 ------------------------- USER UNVISIBLE CHANGES o LinkedTo Rcpp; added C++ STL lower bound function which is reqired for determining overlapping q1 and q3 SWATH windows CHANGES IN VERSION 1.1.13 ------------------------- USER VISIBLE CHANGES o fixed man pages CHANGES IN VERSION 1.1.12 ------------------------- USER VISIBLE CHANGES o impoved package vignette CHANGES IN VERSION 1.1.11 ------------------------- USER VISIBLE CHANGES o modified default parameters of genSwathIonLib o add content to vignette CHANGES IN VERSION 1.1.10 ------------------------- USER VISIBLE CHANGES o added generate.consensus CHANGES IN VERSION 1.1.9 ------------------------- USER VISIBLE CHANGES o new features in specLSet 'summary' plot USER UNVISIBLE CHANGES o refactored merge.specLSet; merge by group_id o added unit test for merge.specLSet CHANGES IN VERSION 1.1.8 ------------------------- USER VISIBLE CHANGES o renamed annotateProteinID to annotate.protein_id o added graphics on plot.specLSet method USER UNVISIBLE CHANGES o refactored merge CHANGES IN VERSION 1.1.7 ------------------------- USER VISIBLE CHANGES o introduce peakplot for bibliospec object o introduce LCMS map for bibliospec object o vignette cosmetics CHANGES IN VERSION 1.1.6 ------------------------- USER VISIBLE CHANGES o introduce specL_bibliospec summary method CHANGES IN VERSION 1.1.5 ------------------------- USER VISIBLE CHANGES o specLSet merge function o work on specLSet summary method CHANGES IN VERSION 1.1.4 ------------------------- USER VISIBLE CHANGES o summary method of specLSet class USER UNVISIBLE CHANGES o unit test for data containing no iRT peptides CHANGES IN VERSION 1.1.3 ------------------------- USER VISIBLE CHANGES o renamed write.Spectronaut to write.spectronaut o write.spectronaut writes filename o added benchmark section in package vignette CHANGES IN VERSION 1.1.2 ------------------------- USER VISIBLE CHANGES o uses modSeq in group_id iff existing CHANGES IN VERSION 1.1.1 ------------------------- USER VISIBLE CHANGES o streamline modsequence, e.g., AAAMASATTM[+16.0]LTTK for compatibility with peakView V2.0 CHANGES IN VERSION 0.99.23 ------------------------- USER VISIBLE CHANGES o added methods for specLSet class: ionlibrary, rt.input, rt.normalized o fixed Sys.time() units in message. USER UNVISIBLE CHANGES o genSwathIonLib using bpmapply CHANGES IN VERSION 0.99.22 ------------------------- USER VISIBLE CHANGES o specLSet plot method CHANGES IN VERSION 0.99.21 ------------------------- USER VISIBLE CHANGES o specLSet class o replace print by show and write.Spectronaut method in specL and specLSet classes CHANGES IN VERSION 1.1.5 ------------------------- USER VISIBLE CHANGES o specLSet merge function o work on specLSet summary method CHANGES IN VERSION 1.1.4 ------------------------- USER VISIBLE CHANGES o summary method of specLSet class USER UNVISIBLE CHANGES o unit test for data containing no iRT peptides CHANGES IN VERSION 1.1.3 ------------------------- USER VISIBLE CHANGES o renamed write.Spectronaut to write.spectronaut o write.spectronaut writes filename o added benchmark section in package vignette CHANGES IN VERSION 1.1.2 ------------------------- USER VISIBLE CHANGES o uses modSeq in group_id iff existing CHANGES IN VERSION 1.1.1 ------------------------- USER VISIBLE CHANGES o streamline modsequence, e.g., AAAMASATTM[+16.0]LTTK for compatibility with peakView V2.0 CHANGES IN VERSION 0.99.23 ------------------------- USER VISIBLE CHANGES o added methods for specLSet class: ionlibrary, rt.input, rt.normalized o fixed Sys.time() units in message. USER UNVISIBLE CHANGES o genSwathIonLib using bpmapply CHANGES IN VERSION 0.99.22 ------------------------- USER VISIBLE CHANGES o specLSet plot method CHANGES IN VERSION 0.99.21 ------------------------- USER VISIBLE CHANGES o specLSet class o replace print by show and write.Spectronaut method in specL and specLSet classes CHANGES IN VERSION 0.99.20 ------------------------- USER VISIBLE CHANGES o replaced mclapply by BiocParalle::bplapply o print method o include iRTpeptide data