Synapter 2.5

Changes in version 2.5.2

Changes in version 2.5.0

  • New version for Bioconductor devel

Synapter 2.4

Changes in version 2.4.0

  • New version for Bioconductor release

Synapter 2.3

Changes in version 2.3.1

  • Partly revert 95f4094 because MSnbase:::utils.applyColumnwiseByGroup is gone.
  • Use html_document instead of html_document2 in the vignettes [2018-01-17].

Synapter 2.1

Changes in version 2.1.1

  • Partly revert 95f4094 because MSnbase:::utils.applyColumnwiseByGroup is gone.

Synapter 2.0

  • Version bump for Bioc release version 3.5.

Synapter 1.99

Changes in version 1.99.2

  • update show,MasterPeptides to check of there’s a fragmentlibrary slot before trying to access it <2017-04-19 Wed>

Changes in version 1.99.1

  • update NEWS file <2017-04-11 Tue>

Changes in version 1.99.0

New features

Ion mobility/Grid search.

  • Replace 2D grid search (retention time, m/z) of synapter1 by 3D grid search (retention time, m/z, ion mobility); set argument imdiff = Inf to get the original 2D grid search; closes #33.
  • Add {set,get}ImDiff methods.
  • getGrid returns an array instead of a matrix (because of the new 3D grid search) [2014-05-16 Fri].
  • plotFeatures(..., what = "all") gains a new argument: “ionmobilty” to plot m/z vs ionmobility as well. [2014-05-16 Fri]
  • plotGrid gets a new argument “maindim” to decided which of the three dimension should be used. [2014-05-16 Fri]
  • Add filterNonUniqueIdentMatches to remove matches of multiple identification data to a single quantitation entry (see #111 for details) [2016-02-22 Mon].

Fragment matching

  • Load identification fragments (final_fragments.csv) and quantitation spectra (Spectrum.xml) via Synapter constructor.
  • New functions: fragmentMatchingPerformance, filterUniqueMatches, filterNonUniqueMatches, filterFragments, plotCumulativeNumberOfFragments, plotFragmentMatchingPerformance, getIdentificationFragments and getQuantitationSpectra.
  • Integrate a fragment library into master objects; closes #63 and #74.

Misc

  • Allow to use an RDS instead of a fasta file as ‘Unique Peptides Database’, adds createUniquePeptideDbRds; closes #55 [2014-04-29 Tue].
  • Introduce IisL argument to dbUniquePeptideSet which treats I/L as same aminoacid if IisL == TRUE (default: IisL = FALSE); closes #60 [2014-04-30 Wed].
  • Add rescueEMRTs functions; replaces the argument mergedEMRTs in findEMRTs; closes #93 [2015-07-26 Sun].
  • Add synergise2 which combines the integrates the new 3D grid search, the fragment matching; and uses slightly different default arguments than synergise1; closes #119 [2016-10-25 Di].
  • Load isotopic distributions from Pep3D data and also export them to MSnSet, to allow the correction of detector saturation; closes #39 [2015-03-29 Sun].
  • Add synapterPlgsAgreement to find agreement between synapter and PLGS; closes #73.
  • Introduce modelIntensity to correct systematic intensity shifts (similar to modelRt); closes #116.

Improvements

  • Extract the ion that was used for identification (isFid == 1) from the Pep3D file instead of the first instance [2014-05-13 Tue].
  • Add updateObject and validObject method [2014-11-16 Sun].
  • Rename QuantPep3DData$Function column into QuantPep3DData$matchedEMRTs; closes #67 [2015-07-26 Sun].
  • Use just unique peptides in master creation (see #107) [2016-01-23 Sat].
  • New rmarkdown based reports for synergise1 (synonym to synergise) and synergise2.

Bugfixes

  • Use new loess model in master creation (now based on m-estimator instead of least squares, identical to retention time model in classical synergise workflow; see #107 for details) [2016-01-23 Sat]
  • Fix retention time model calculation in plotFeatures(..., what="some") [2014-04-28 Mon].

Internal changes

  • Add testthat to Suggests [2014-04-25 Fri].
  • Add recommended biocView [2014-06-05 Thu].
  • Replace any(is.na(...) by anyNA(...); synapter depends on R >= 3.1.0 now [2014-11-01 Sat].
  • Add ClassVersion field to Synapter class [2014-11-21 Fri].
  • Add Versioned class as parent class to MasterPeptides and MasterFdrResults [2014-11-22 Sat].
  • Adapt synergise to new grid search (closes #81) [2016-10-16 So].
  • Replace hwriter by rmarkdown report in synergise; closes #120. [2016-10-17 Mon]

Removed functions/arguments

  • Remove synapterGUI.
  • Remove unused internal functions: filterCommonSeq, filterKeepUniqueSeq, filterKeepUniqueProt [2014-11-27 Thu].
  • Remove “mergedEMRTs” argument from findEMRTs. Now rescueEMRTs has to be called manually at the end of the processing; close #93 [2015-07-26 Sun]
  • Remove “light” version of writeMergedPeptides and writeMachtedPeptides (now always the full data.frame is saved; see #95) [2016-10-16 Sun]
  • Update synapterTiny and synapterTinyData [2016-10-16 So]

Synapter 1.13

Changes in version 1.13.1

  • Update call to nQuants to accomodate changes in MSnbase (see commit #ce637b87e491a2f4c9f93490b2f4c7027cbfce16) <2016-02-29 Mon>
  • Defunct synapterGUI <2016-02-29 Mon>

Changes in version 1.13.0

  • Bioc devel 3.2

Synapter 1.12

Changes in version 1.12.0

  • Bioc release 3.1

Synapter 1.11

Changes in version 1.11.2

Changes in version 1.11.1

Synapter 1.9

Changes in version 1.9.5

  • update cross reference to qvalue::plot.qvalue in Synapter man page; closes #86 [2015-03-31 Tue]

Changes in version 1.9.4

  • use biocstyle [2015-01-23 Fri]
  • use requireNamespace [2015-01-23 Fri]

Changes in version 1.9.3

  • Filter entries in quantiation final peptides and Pep3D data that don’t match in their intensity valus; see #42 for details. [2014-11-26 Wed]

Changes in version 1.9.2

  • Only suggesting tcltk and tcltk2, as gui is now deprecated [2014-11-21 Fri]

Changes in version 1.9.1

  • Deprecating synatperGUI [2014-11-10 Mon]
  • Directing questions to the Bioc support site [2014-11-10 Mon]

Changes in version 1.9.0

  • new devel version for Bioc 3.1

Synapter 1.7

Changes in version 1.7.0

  • Deprecating synatperGUI [2014-11-10 Mon]
  • Directing questions to the Bioc support site [2014-11-10 Mon]

Synapter 1.5

Changes in version 1.5.7

  • Enable setting number of missed cleavages (closes #53) [2014-03-24 Mon]

Changes in version 1.5.6

  • change the default value of grid.ppm.from to 2 (was 5 before) [2014-03-05 Wed]
  • change the separator in GridDetails’ names to “:” (was “.” before) [2014-03-07 Fri]
  • test for corresponding Pep3D file (closes #42) [2014-03-19 Wed]

Changes in version 1.5.5

  • fix a bug in the calculation of non unique matches in gridSearch2 (part of searchGrid); results in a higher number of non unique matches (some of the reported -2 will now be reported as 2 in the grid details) [2014-03-05 Wed]
  • partial rewrite of gridSearch2 (part of searchGrid) for faster grid calculation [2014-03-04 Tue]

Changes in version 1.5.4

  • biocViews update

Changes in version 1.5.3

  • modified findMSeEMRTs (part of searchGrid) for faster grid calculation [2014-02-28 Fri]
  • typos in manual [2014-02-25 Tue]
  • replace readFasta by Biostrings::readAAStringSet [2014-02-25 Tue]
  • replace digest by cleaver::cleave [2014-02-25 Tue]

Changes in version 1.5.1

  • typo in vignette [2014-02-18 Tue]

Changes in version 1.5.0

  • new devel version for Bioc 2.14

Synapter 1.3

Changes in version 1.3.4

  • estimateMasterFdr now support list of vector as pepfiles [2013-09-27 Fri]
  • import(MSnbase) [2013-09-27 Fri]

Changes in version 1.3.3

  • Updated references. [2013-07-05 Fri]

Changes in version 1.3.2

  • fixed bug when using findEMRTs = “copy” [2013-05-30 Thu]

Changes in version 1.3.1

  • Reporting total number of peptides in dbUniquePeptideSet. Fixes issue #41. [2013-05-13 Mon]
  • New mergedEMRTs arg in findEMRTs. Closes issue #38. [2013-05-13 Mon]
  • fixed synapterTiny\$QuantPep3DData, which had the rownames as first column synapterTiny\$QuantPep3DData\$X. Detected thanks to new mergedEMRTs arg. [2013-05-13 Mon]
  • added mergedEMRTs arg to synergise [2013-05-22 Wed]
  • Synapter checks that one file per list element is passed [2013-05-28 Tue]
  • minor typo/fixes [2013-05-28 Tue]
  • new idSource column when matching EMRTs [2013-05-29 Wed]
  • new performance2 method that shows identification source and NA values contingency table [2013-05-29 Wed]
  • new filterPeptideLength method [2013-05-29 Wed]
  • added peplen argument to synergise to filter
  • n peptide length [2013-05-29 Wed]

Changes in version 1.3.0

  • Bioc 2.13 devel version bump

Synapter 1.2

Changes in version 1.2.0

  • Bioc 2.12 stable version bump

Synapter 1.1

Changes in version 1.1.5

  • updated references [2013-03-22 Fri]

Changes in version 1.1.4

  • added citation [2013-03-21 Thu]
  • vignette uses knitr engine and scrartcl class [2013-03-21 Thu]

Changes in version 1.1.3

  • knitr 1.0 compatibility, based on Dan’s updates [2013-01-15 Tue]

Changes in version 1.1.2

  • added note about tcl BWidget package in synapterGUI man [2012-10-04 Thu]

Changes in version 1.1.1

  • fixing vignette [2012-10-02 Tue]

Changes in version 1.1.0

  • new devel version bump [2012-10-01 Mon]