BiocManager::install [2018-07-16].imdiff = Inf to get the original 2D grid search; closes #33.{set,get}ImDiff methods.getGrid returns an array instead of a matrix (because of the new 3D grid search) [2014-05-16 Fri].plotFeatures(..., what = "all") gains a new argument: “ionmobilty” to plot m/z vs ionmobility as well. [2014-05-16 Fri]plotGrid gets a new argument “maindim” to decided which of the three dimension should be used. [2014-05-16 Fri]filterNonUniqueIdentMatches to remove matches of multiple identification data to a single quantitation entry (see #111 for details) [2016-02-22 Mon].final_fragments.csv) and quantitation spectra (Spectrum.xml) via Synapter constructor.fragmentMatchingPerformance, filterUniqueMatches, filterNonUniqueMatches, filterFragments, plotCumulativeNumberOfFragments, plotFragmentMatchingPerformance, getIdentificationFragments and getQuantitationSpectra.createUniquePeptideDbRds; closes #55 [2014-04-29 Tue].IisL argument to dbUniquePeptideSet which treats I/L as same aminoacid if IisL == TRUE (default: IisL = FALSE); closes #60 [2014-04-30 Wed].rescueEMRTs functions; replaces the argument mergedEMRTs in findEMRTs; closes #93 [2015-07-26 Sun].synergise2 which combines the integrates the new 3D grid search, the fragment matching; and uses slightly different default arguments than synergise1; closes #119 [2016-10-25 Di].synapterPlgsAgreement to find agreement between synapter and PLGS; closes #73.modelIntensity to correct systematic intensity shifts (similar to modelRt); closes #116.isFid == 1) from the Pep3D file instead of the first instance [2014-05-13 Tue].updateObject and validObject method [2014-11-16 Sun].QuantPep3DData$Function column into QuantPep3DData$matchedEMRTs; closes #67 [2015-07-26 Sun].rmarkdown based reports for synergise1 (synonym to synergise) and synergise2.plotFeatures(..., what="some") [2014-04-28 Mon].testthat to Suggests [2014-04-25 Fri].any(is.na(...) by anyNA(...); synapter depends on R >= 3.1.0 now [2014-11-01 Sat].ClassVersion field to Synapter class [2014-11-21 Fri].Versioned class as parent class to MasterPeptides and MasterFdrResults [2014-11-22 Sat].synergise to new grid search (closes #81) [2016-10-16 So].hwriter by rmarkdown report in synergise; closes #120. [2016-10-17 Mon]synapterGUI.filterCommonSeq, filterKeepUniqueSeq, filterKeepUniqueProt [2014-11-27 Thu].findEMRTs. Now rescueEMRTs has to be called manually at the end of the processing; close #93 [2015-07-26 Sun]writeMergedPeptides and writeMachtedPeptides (now always the full data.frame is saved; see #95) [2016-10-16 Sun]synapterTiny and synapterTinyData [2016-10-16 So]