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 <URL:
https://cran.r-project.org/package=protViz>
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 <URL:
http://bioconductor.org/packages/devel/bioc/vignettes/specL/inst/doc/report.html>.
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 <URL:
http://bioconductor.org/packages/release/bioc/vignettes/specL/inst/doc/cdsw.html>
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