NEWS
topdownr 1.33
Changes in version 1.33.1
- Adapt to changes in ggplot2.
- Adapt
.calculateFragments to changes in PSMatch::calculateFragments
introduced in
PSMatch:PR41.
topdownr 1.31
Changes in version 1.31.1
- Move package to codeberg.org.
topdownr 1.29
Changes in version 1.29.1
- Adapt
.calculateFragments to changes in PSMatch::calculateFragments
introduced in
PSMatch:PR19.
- Replace partial matching arguments with complete argument names.
topdownr 1.25
Changes in version 1.25.1
- New version for Bioc 3.19 (devel)
- Adapt to fragment functions that are moved from
MSnbase to PSMatch.
Changes in version 1.19.2
topdownr 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.
topdownr 1.18
- New version for Bioc 3.14 (release)
topdownr 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
Changes in version 1.17.1
- New version for Bioc 3.15 (devel)
- Adapt to new
DFrame.
topdownr 1.16
- New version for Bioc 3.14 (release)
topdownr 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].
topdownr 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 [email protected] [2021-03-15].
topdownr 1.12
- New version for Bioc 3.12 (release)
topdownr 1.11
- New version for Bioc 3.12 (devel)
topdownr 1.10
- New version for Bioc 3.11 (release)
topdownr 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].
topdownr 1.8
- New version for Bioc 3.10 (release)
topdownr 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].
topdownr 1.6
- New version for Bioc 3.9 (release)
topdownr 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
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].
topdownr 1.4
- New version for Bioc 3.8 (release)
topdownr 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)
topdownr 1.2
Changes in version 1.2.0
- New version for Bioc 3.7 (release)
topdownr 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)
topdownr 1.0
Changes in version 1.0.0
- New version for Bioc 3.6 (release)
topdownr 0.9
Changes in version 0.99.0