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
<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
<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
<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