# 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 - First public release.