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