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.