Changes in version 1.17.22 (2019-01-24) o code cosmetics to eliminate ERRORS and WARNINGS in R CMD BiocCheck of version 3.9. Changes in version 1.13.02 (2017-11-20) o Eliminated C++-11 and Rcpp linking. Passing unit tests. o use lower_bound_ function exported by Changes in version 1.9.15 (2017-04-21) o added prozor (>= 0.2.2) to the Suggest list. o added more specific R package version numbers in DESCRIPTION file. o in plot.specLSet (normalized RT versus RT) use pch=16 and color with parameter alpha=0.1. o fixed issue #22 by including the iRTs in the ionlibrary; LIB <- genSwathIonLib(data=peptideStd, data.fit=peptideStd.redundant); LIB@input.parameter$iRTpeptides. o fixed issue #19. o removed par command in specLset plot function. o added vignettes/report.Rmd file, see also . Changes in version 1.7.4 (2016-05-19) o USER VISIBLE CHANGES • added to specLSet summary "which std peptides (iRTs) where found in which raw files" • one plot per raw file in plot methode of specLSet object Changes in version 1.7.1 (2016-05-13) o USER VISIBLE CHANGES • replaced NEWS by NEWS.Rd file • modified specL object /replace decoy by score attribute #1,#4 • specL on BioC 3.3 Changes in version 1.5.10-13 o USER UNVISIBLE CHANGES • added specLSet class support for cdsw methode • changed Rmd5 vignette style • added cdsw test case • intro new vignette for cdsw method Changes in version 1.5.9 o USER UNVISIBLE CHANGES • added test case for read.biliospec Changes in version 1.5.5 o USER VISIBLE CHANGES • added RT prediction vignette file Changes in version 1.5.4 o USER UNVISIBLE CHANGES • changed NAMESPACES and read.bibliospec docu to avoid warnings in 3.3 check Changes in version 1.5.3 o USER UNVISIBLE CHANGES • added sqlite files for peptideStd RData #13 Changes in version 1.5.2 o USER UNVISIBLE CHANGES • find all signals having two or more in-silico fragment ions. #8 • keep only the nearest fragment ion; if there are more take the first in line Changes in version 1.3.7 o USER UNVISIBLE CHANGES • getProteinPeptideTable - added Changes in version 1.3.5 o USER UNVISIBLE CHANGES • read.bibliospec - bugfixes Changes in version 1.3.4 o USER VISIBLE CHANGES • added Witold Wolski as maintainer o USER UNVISIBLE CHANGES • read.bibliospec - replaced old code (for loop) by using mcmapply • added time meassurements to read.bibliospec Changes in version 1.3.3 o USER VISIBLE CHANGES • plot::specLSet draws alpha circles iff plot(..., art=TRUE) o USER UNVISIBLE CHANGES • .mascot2psmSet buxfix • renamed column name in spectronaut outpu from irt to irt_or_rt Changes in version 1.3.2 o USER VISIBLE CHANGES • added ssrc (Sequence Specific Retention Calculator) function • added a CITATION file Changes in version 1.3.1 o USER VISIBLE CHANGES • added fucntion cdsw o USER UNVISIBLE CHANGES • modified unit test for genSwathIonLib Changes in version 1.1.17 o USER UNVISIBLE CHANGES • removed file argument in genSwathIonLib function Changes in version 1.1.16 o USER UNVISIBLE CHANGES • added unit test for genSwathIonLib Changes in version 1.1.15 o USER UNVISIBLE CHANGES • added circle plots to specLSet plot method • added breaks argument in genSwathIonLib methode Changes in version 1.1.14 o USER UNVISIBLE CHANGES • 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 o USER VISIBLE CHANGES • fixed man pages Changes in version 1.1.12 o USER VISIBLE CHANGES • impoved package vignette Changes in version 1.1.11 o USER VISIBLE CHANGES • modified default parameters of genSwathIonLib • add content to vignette Changes in version 1.1.10 o USER VISIBLE CHANGES • added generate.consensus Changes in version 1.1.9 o USER VISIBLE CHANGES • new features in specLSet 'summary' plot o USER UNVISIBLE CHANGES • refactored merge.specLSet; merge by group_id • added unit test for merge.specLSet Changes in version 1.1.8 o USER VISIBLE CHANGES • renamed annotateProteinID to annotate.protein_id • added graphics on plot.specLSet method o USER UNVISIBLE CHANGES • refactored merge Changes in version 1.1.7 o USER VISIBLE CHANGES • introduce peakplot for bibliospec object • introduce LCMS map for bibliospec object • vignette cosmetics Changes in version 1.1.6 o USER VISIBLE CHANGES • introduce specL_bibliospec summary method Changes in version 1.1.5 o USER VISIBLE CHANGES • specLSet merge function • work on specLSet summary method Changes in version 1.1.4 o USER VISIBLE CHANGES • summary method of specLSet class o USER UNVISIBLE CHANGES • unit test for data containing no iRT peptides Changes in version 1.1.3 o USER VISIBLE CHANGES • renamed write.Spectronaut to write.spectronaut • write.spectronaut writes filename • added benchmark section in package vignette Changes in version 1.1.2 o USER VISIBLE CHANGES • uses modSeq in group_id iff existing Changes in version 1.1.1 o USER VISIBLE CHANGES • streamline modsequence, e.g., AAAMASATTM[+16.0]LTTK for compatibility with peakView V2.0 Changes in version 0.99.23 o USER VISIBLE CHANGES • added methods for specLSet class: ionlibrary, rt.input, rt.normalized • fixed Sys.time() units in message. o USER UNVISIBLE CHANGES • genSwathIonLib using bpmapply Changes in version 0.99.22 o USER VISIBLE CHANGES • specLSet plot method Changes in version 0.99.21 o USER VISIBLE CHANGES • specLSet class • replace print by show and write.Spectronaut method in specL and specLSet classes