NEWS.md
rmarkdown to Suggests:; see https://github.com/yihui/knitr/issues/1864 for details [2021-07-27].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].class(m) now returns c("matrix", "array") in r-devel) [2019-12-17].condition argument [2019-11-22].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]..validFilename and .translateThermoIdToScanId [2019-11-22].defaultMs1Settings and defaultMs2Settings [2019-11-18]..rbind for lists with mixed data.frame and DataFrame [2019-11-18]."AgcTarget" column from colData DataFrame.defaultMs1Settings and defaultMs2Settings. They will be removed in 3.11 [2019-06-19].DataFrame introduced in 1.5.4 (a419f59, c4bfc1c) because they are fixed upstream in S4Vectors. Keep unit tests in place. [2019-03-27].makeRowNames/.colsToLogical/.colsToRle on DataFrame without any numeric/character columns.set.seed (order changed during R-devel upgrade).expandMs1Conditions, expandTms2Conditions, createExperimentsFragmentOptimisation functions to allow more flexibility in method creation; see also #77 [2018-12-07].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].data-generation vignette to the new workflow [2018-12-07].defaultMs1Settings and defaultMs2Settings. They will be defunct in Bioconductor 3.10 and removed in 3.11 [2018-12-07].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].R CMD check [2018-10-10].MSnbase 2.7.2 with internal fragments; see #82 [2018-06-03].”BiocManager::install [2018-07-16].MSnbase 2.7.2 with internal fragments; see #82 [2018-06-03].FragmentViews start/end/width and labels for internal fragments [2018-06-03].as(tds, "MSnSet") unit test [2018-07-06].elementMetadata(..., use.names=FALSE) in combine,FragmentViews,FragmentViews-method to avoid duplicated rownames in elementMetadata slot [2018-07-06].mz,FragmentViews-method [2018-02-01].fragmentMass and fragmentNames functions [2018-02-22]..readMzMl [2018-02-22].FragmentCoverage and BondCoverage columns to bestConditions,NCBSet-method [2018-02-23].plot [2018-01-17].updateMedianInjectionTime,TopDownSet-method to updateMedianInjectionTime,AbstractTopDownSet-method; closes #69; see also #71 [2018-01-27]..matchFragments for length(fmass) == 0 [2018-01-27].TopDownSet see #70 [2018-01-27].combine,FragmentViews,FragmentViews-method [2018-01-27].combine TopDownSet objects with different fragment types; closes #71 [2018-01-27].all.equal for AbstractTopDownSet objects [2018-01-27].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].basename was used) in AbstractTopDownSet objects [2017-12-28].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].combine and documentation [2017-12-28].tds example data set to reflect changes in colData introduced in version 1.1.2 [2017-12-28].conditionNames,AbstractTopDownSet-method to access rownames(colData(tds)) [2017-12-23].updateConditionNames,AbstractTopDownSet-method (closes #60) [2017-12-23].updateMedianInjectionTime,TopDownSet-method into updateMedianInjectionTime,AbstractTopDownSet-method to work with TopDownSet and NCBSet objects [2017-12-27].combine,AbstractTopDownSet-method to combine multiple TopDownSet/NCBSet objects (closes #69) [2017-12-28]..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].colData [2017-12-22].character columns in scan and method information to logical [2017-12-22]..camelCase to avoid “TIC” to “TIc” and “UseCalibratedUVPDTimeMs2” to “UseCalibrateduvpdTimems2” conversion (now: “Tic” and “UseCalibratedUvpdTimeMs2”) [2017-12-22].bestConditions,NCBSet-method and fragmentationMap (closes #62) [2017-12-02]..readScanHeadsTable to avoid error if any is missing (fixes #68) [2017-12-20].colData (even not if readTopDownFiles(..., dropNonInformativeColumns=TRUE)) [2017-12-20].fragmentationMap,NCBSet-method [2017-12-20].updateMedianInjectionTime,TopDownSet-method (closes #66) [2017-12-20].