NEWS

---

specL 1.17.22 (2019-01-24)

• code cosmetics to eliminate ERRORS and WARNINGS in R CMD BiocCheck of version 3.9.

specL 1.13.02 (2017-11-20)

• Eliminated C++-11 and Rcpp linking. Passing unit tests.

• use lower_bound_ function exported by https://cran.r-project.org/package=protViz

specL 1.9.15 (2017-04-21)

• added prozor (>= 0.2.2) to the Suggest list.

• added more specific R package version numbers in DESCRIPTION file.

• in plot.specLSet (normalized RT versus RT) use pch=16 and color with parameter alpha=0.1.

• fixed issue #22 by including the iRTs in the ionlibrary; LIB <- genSwathIonLib(data=peptideStd, data.fit=peptideStd.redundant); [email protected]$iRTpeptides.

• fixed issue #19.

• removed par command in specLset plot function.

• added vignettes/report.Rmd file, see also http://bioconductor.org/packages/devel/bioc/vignettes/specL/inst/doc/report.html.

specL 1.7.4 (2016-05-19)

• 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

specL 1.7.1 (2016-05-13)

• USER VISIBLE CHANGES

  • replaced NEWS by NEWS.Rd file

  • modified specL object /replace decoy by score attribute #1,#4

  • specL on BioC 3.3

specL 1.5.10-13

• 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

specL 1.5.9

• USER UNVISIBLE CHANGES

  • added test case for read.biliospec

specL 1.5.5

• USER VISIBLE CHANGES

  • added RT prediction vignette file

specL 1.5.4

• USER UNVISIBLE CHANGES

  • changed NAMESPACES and read.bibliospec docu to avoid warnings in 3.3 check

specL 1.5.3

• USER UNVISIBLE CHANGES

  • added sqlite files for peptideStd RData #13

specL 1.5.2

• 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

specL 1.3.7

• USER UNVISIBLE CHANGES

  • getProteinPeptideTable - added

specL 1.3.5

• USER UNVISIBLE CHANGES

  • read.bibliospec - bugfixes

specL 1.3.4

• USER VISIBLE CHANGES

  • added Witold Wolski as maintainer

• USER UNVISIBLE CHANGES

  • read.bibliospec - replaced old code (for loop) by using mcmapply

  • added time meassurements to read.bibliospec

specL 1.3.3

• USER VISIBLE CHANGES

  • plot::specLSet draws alpha circles iff plot(..., art=TRUE)

• USER UNVISIBLE CHANGES

  • .mascot2psmSet buxfix

  • renamed column name in spectronaut outpu from irt to irt_or_rt

specL 1.3.2

• USER VISIBLE CHANGES

  • added ssrc (Sequence Specific Retention Calculator) function

  • added a CITATION file

specL 1.3.1

• USER VISIBLE CHANGES

  • added fucntion cdsw

• USER UNVISIBLE CHANGES

  • modified unit test for genSwathIonLib

specL 1.1.17

• USER UNVISIBLE CHANGES

  • removed file argument in genSwathIonLib function

specL 1.1.16

• USER UNVISIBLE CHANGES

  • added unit test for genSwathIonLib

specL 1.1.15

• USER UNVISIBLE CHANGES

  • added circle plots to specLSet plot method

  • added breaks argument in genSwathIonLib methode

specL 1.1.14

• USER UNVISIBLE CHANGES

  • LinkedTo Rcpp; added C++ STL lower bound function which is reqired for determining overlapping q1 and q3 SWATH windows

specL 1.1.13

• USER VISIBLE CHANGES

  • fixed man pages

specL 1.1.12

• USER VISIBLE CHANGES

  • impoved package vignette

specL 1.1.11

• USER VISIBLE CHANGES

  • modified default parameters of genSwathIonLib

  • add content to vignette

specL 1.1.10

• USER VISIBLE CHANGES

  • added generate.consensus

specL 1.1.9

• USER VISIBLE CHANGES

  • new features in specLSet 'summary' plot

• USER UNVISIBLE CHANGES

  • refactored merge.specLSet; merge by group_id

  • added unit test for merge.specLSet

specL 1.1.8

• USER VISIBLE CHANGES

  • renamed annotateProteinID to annotate.protein_id

  • added graphics on plot.specLSet method

• USER UNVISIBLE CHANGES

  • refactored merge

specL 1.1.7

• USER VISIBLE CHANGES

  • introduce peakplot for bibliospec object

  • introduce LCMS map for bibliospec object

  • vignette cosmetics

specL 1.1.6

• USER VISIBLE CHANGES

  • introduce specL_bibliospec summary method

specL 1.1.5

• USER VISIBLE CHANGES

  • specLSet merge function

  • work on specLSet summary method

specL 1.1.4

• USER VISIBLE CHANGES

  • summary method of specLSet class

• USER UNVISIBLE CHANGES

  • unit test for data containing no iRT peptides

specL 1.1.3

• USER VISIBLE CHANGES

  • renamed write.Spectronaut to write.spectronaut

  • write.spectronaut writes filename

  • added benchmark section in package vignette

specL 1.1.2

• USER VISIBLE CHANGES

  • uses modSeq in group_id iff existing

specL 1.1.1

• USER VISIBLE CHANGES

  • streamline modsequence, e.g., AAAMASATTM[+16.0]LTTK for compatibility with peakView V2.0

specL 0.99.23

• USER VISIBLE CHANGES

  • added methods for specLSet class: ionlibrary, rt.input, rt.normalized

  • fixed Sys.time() units in message.

• USER UNVISIBLE CHANGES

  • genSwathIonLib using bpmapply

specL 0.99.22

• USER VISIBLE CHANGES

  • specLSet plot method

specL 0.99.21

• USER VISIBLE CHANGES

  • specLSet class

  • replace print by show and write.Spectronaut method in specL and specLSet classes