Changes in version 1.19
Changes in version 1.19.2
- Avoid coercion methods that will be deprecated in Matrix 1.4-2.
- Replace stopifnot calls with if (...) stop calls.
Changes in version 1.19.1
- New version for Bioc 3.17 (devel)
- Rerun latest roxygen2.
- Remove if (getGeneric(...)) statements in AllGenerics.R do avoid
problems while reloading the package.
Changes in version 1.18
- New version for Bioc 3.14 (release)
Changes in version 1.17
Changes in version 1.17.3
- Depending on mzR 2.27.5.
- Fix unit test for .readSpectrum to adapt to new mzR 2.27.5.
Changes in version 1.17.2
- Fix roxygen2 warnings.
Changes in version 1.17.1
- New version for Bioc 3.15 (devel)
- Adapt to new DFrame.
Changes in version 1.16
- New version for Bioc 3.14 (release)
Changes in version 1.15
Changes in version 1.15.1
- Add rmarkdown to Suggests:; see
https://github.com/yihui/knitr/issues/1864 for details [2021-07-27].
Changes in version 1.13
- New version for Bioc 3.13 (devel)
Changes in version 1.13.1
- as(..., "NCBSet") now treats neutral losses and modifications as
bonds as well.
- readTopDownFiles gains a new argument customModifications to allow
user-defined modifications. Suggestion and first implementation by
Maša Babović masab@bmb.sdu.dk [2021-03-15].
Changes in version 1.12
- New version for Bioc 3.12 (release)
Changes in version 1.11
- New version for Bioc 3.12 (devel)
Changes in version 1.10
- New version for Bioc 3.11 (release)
Changes in version 1.9
- New version for Bioc 3.11 (devel)
Changes in version 1.9.4
- Fix unit tests that check for "matrix" class. (class(m) now returns
c("matrix", "array") in r-devel) [2019-12-17].
Changes in version 1.9.3
- Adapt analysis vignette to changed condition argument [2019-11-22].
Changes in version 1.9.2
- Set conditions="ScanDescription" as new default for
readTopDownFiles. The creation of FilterString IDs in the method
files was deprecated since over a year. conditions="FilterString" is
still possible for backward-compatibility [2019-11-22].
- Fix error message handling in .validFilename and
.translateThermoIdToScanId [2019-11-22].
Changes in version 1.9.1
- Remove defaultMs1Settings and defaultMs2Settings [2019-11-18].
- Fix .rbind for lists with mixed data.frame and DataFrame
[2019-11-18].
Changes in version 1.8
- New version for Bioc 3.10 (release)
Changes in version 1.7
- New version for Bioc 3.10 (devel)
Changes in version 1.7.2
- Add readTopDownSet(..., conditions="ScanDescription") as a new way
to read scan conditions (see #80/#81) [2019-08-08].
Changes in version 1.7.1
- Remove NEWS file (just keep NEWS.md).
- Never remove "AgcTarget" column from colData DataFrame.
- Strip white spaces from ScanHeadsman output.
- Defunct defaultMs1Settings and defaultMs2Settings. They will be
removed in 3.11 [2019-06-19].
Changes in version 1.6
- New version for Bioc 3.9 (release)
Changes in version 1.5
- New version for Bioc 3.9 (devel)
Changes in version 1.5.6
- Revert changes for NULL indices of DataFrame introduced in 1.5.4
(a419f59, c4bfc1c) because they are fixed upstream in S4Vectors.
Keep unit tests in place. [2019-03-27]
Changes in version 1.5.5
- Depends on R >= 3.5.0 now, because the seralization format changed
in R.
Changes in version 1.5.4
- Fix for internal .makeRowNames/.colsToLogical/.colsToRle on
DataFrame without any numeric/character columns.
- Fix unit test that uses set.seed (order changed during R-devel
upgrade).
Changes in version 1.5.3
- biocViews: ImmunoOncology added by Kayla-Morrell
kayla.morrell@roswellpark.org [2019-01-04].
Changes in version 1.5.2
- Add expandMs1Conditions, expandTms2Conditions,
createExperimentsFragmentOptimisation functions to allow more
flexibility in method creation; see also #77 [2018-12-07].
- Modify interface/arguments of writeMethodXmls to adapt to new method
creation workflow (the old interface will be defunct in
Bioconductor 3.10 and removed in 3.11) [2018-12-07].
- Adapt the data-generation vignette to the new workflow [2018-12-07].
- Deprecated defaultMs1Settings and defaultMs2Settings. They will be
defunct in Bioconductor 3.10 and removed in 3.11 [2018-12-07].
Changes in version 1.5.1
- readTopDownFiles gains the argument conditions to control wheter
"FilterStrings" or a given number of conditions is used to create
condition IDs; see #77 [2018-11-07].
Changes in version 1.4
- New version for Bioc 3.8 (release)
Changes in version 1.3
Changes in version 1.3.6
- Add Pavel's and Ole's ORCID to DESCRIPTION [2018-10-23].
Changes in version 1.3.5
- Fix format of roxygen links to foreign packages to avoid link
warning in R CMD check [2018-10-10].
Changes in version 1.3.4
- Add inst/CITATION file [2018-09-26].
Changes in version 1.3.3
- Revert commit c6e8dfd: "Adapt to MSnbase 2.7.2 with internal
fragments; see #82 [2018-06-03]."
Changes in version 1.3.2
- Use BiocManager::install [2018-07-16].
Changes in version 1.3.1
- Adapt to MSnbase 2.7.2 with internal fragments; see #82
[2018-06-03].
- Fix FragmentViews start/end/width and labels for internal fragments
[2018-06-03].
- Fix as(tds, "MSnSet") unit test [2018-07-06].
- Use elementMetadata(..., use.names=FALSE) in
combine,FragmentViews,FragmentViews-method to avoid duplicated
rownames in elementMetadata slot [2018-07-06].
Changes in version 1.3.0
- New version for Bioc 3.8 (devel)
Changes in version 1.2
Changes in version 1.2.0
- New version for Bioc 3.7 (release)
Changes in version 1.1
Changes in version 1.1.7
- Add mz,FragmentViews-method [2018-02-01].
- Remove internal fragmentMass and fragmentNames functions
[2018-02-22].
- Parse "spectrumId" column of the mzML header to find the scan number
(instead of the "acquisitionNum") because ProteomDiscover generates
non-standard "spectrumId" and proteowizard fails to translated it
into a valid "acquisitionNum". See #73 for details [2018-02-22].
- Recalculate TotIonCurrent in the main loop of .readMzMl
[2018-02-22].
- Add FragmentCoverage and BondCoverage columns to
bestConditions,NCBSet-method [2018-02-23].
- Use retention times to test for correct matching between
ScanHeadsman .txt output and mzML files; closes #74; [2018-02-23].
Changes in version 1.1.6
- Rotate fragment labels (vertical orientation) in plot [2018-01-17].
- Replace signature for updateMedianInjectionTime,TopDownSet-method to
updateMedianInjectionTime,AbstractTopDownSet-method; closes #69; see
also #71 [2018-01-27].
- Fix .matchFragments for length(fmass) == 0 [2018-01-27].
- Just plot fragments that are present in current TopDownSet see #70
[2018-01-27].
- Add combine,FragmentViews,FragmentViews-method [2018-01-27].
- Allow to combine TopDownSet objects with different fragment types;
closes #71 [2018-01-27].
- Add all.equal for AbstractTopDownSet objects [2018-01-27].
- Allow the user to decide how to handle redundant fragment matching.
Current default is redundantFragmentMatch="remove" and
redundantIonMatch="remove". This will reduce the number of fragment
matches. Choose "closest" for both to get the old behaviour. See
also #72 [2018-01-29].
- TopDownSet object store the matching tolerance and strategies
(redundantIonMatch, redundantFragmentMatch). AbstractTopDownSet and
NCBSet lost their tolerance slot. Saved objects need to be recreated
[2018-01-30].
- bestConditions,NCBSet-method returns a 5-column matrix now. Colums
are: Index, FragmentsAddedToCombination, BondsAddedToCombination,
FragmentsInCondition, BondsInCondition; see #52 [2018-01-30].
Changes in version 1.1.5
- Keep full filename (before basename was used) in AbstractTopDownSet
objects [2017-12-28].
- Add plot,TopDownSet-method [2017-12-29].
- bestConditions,NCBSet-method gains a new argument maximise that
allows to optimise for number of fragments or bonds covered
(default: "fragments"); see #52 [2018-01-15].
Changes in version 1.1.4
- Add missing export of combine and documentation [2017-12-28].
- Resave tds example data set to reflect changes in colData introduced
in version 1.1.2 [2017-12-28].
Changes in version 1.1.3
- Add conditionNames,AbstractTopDownSet-method to access
rownames(colData(tds)) [2017-12-23].
- Add updateConditionNames,AbstractTopDownSet-method (closes #60)
[2017-12-23].
- Turn updateMedianInjectionTime,TopDownSet-method into
updateMedianInjectionTime,AbstractTopDownSet-method to work with
TopDownSet and NCBSet objects [2017-12-27].
- Add combine,AbstractTopDownSet-method to combine multiple
TopDownSet/NCBSet objects (closes #69) [2017-12-28].
Changes in version 1.1.2
- Add .rbind to combine scan and method information with different
number of colums (could happen when CID/HCD and UVPD scans are taken
independently with different software versions) [2017-12-22].
- Don't replace NA values with zeros in the colData [2017-12-22].
- Convert On/Off character columns in scan and method information to
logical [2017-12-22].
- Fix .camelCase to avoid "TIC" to "TIc" and
"UseCalibratedUVPDTimeMs2" to "UseCalibrateduvpdTimems2" conversion
(now: "Tic" and "UseCalibratedUvpdTimeMs2") [2017-12-22].
Changes in version 1.1.1
- Respect assigned intensity in conditions for
bestConditions,NCBSet-method and fragmentationMap (closes #62)
[2017-12-02].
- Fix explanation of random forest barchart in analysis vignette
[2017-12-02].
- Create all fragmentation methods in .readScanHeadsTable to avoid
error if any is missing (fixes #68) [2017-12-20].
- Never remove Activation column in colData (even not if
readTopDownFiles(..., dropNonInformativeColumns=TRUE)) [2017-12-20].
- Allow UVPD in fragmentationMap,NCBSet-method [2017-12-20].
- Add new method: updateMedianInjectionTime,TopDownSet-method (closes
#66) [2017-12-20].
Changes in version 1.1.0
- New version for Bioc 3.7 (devel)
Changes in version 1.0
Changes in version 1.0.0
- New version for Bioc 3.6 (release)
Changes in version 0.9
Changes in version 0.99.0
- First public release.