Changes in version 1.9 Changes in 1.9.2 - Fix missing ProtGenerics dependency. Changes in 1.9.1 - Add parameter scalePeaks to plotSpectraMirror to allow scaling peak intensities before plotting. Changes in version 1.7 Changes in 1.7.5 - Add parameter addOriginalQueryIndex to matchSpectra() that allows to add an additional spectra variable to the query Spectra with the index in the original object (issue #114). Changes in 1.7.4 - Import setBackend() generic from ProtGenerics. Changes in 1.7.3 - Add SingleMatchParam for filterMatches to allow selection of (at most) a single match to a target element for each query element. - Add new methods queryVariables and targetVariables to extract the names of variables (columns) of query and target. Changes in 1.7.2 - Update the Spectra objects within the package to the new versions. Changes in 1.7.1 - Add examples and a section to the vignette explaining the use of createStandardMixes. Changes in version 1.5 Changes in 1.5.9 - Addition of global function createStandardMixes. Changes in 1.5.8 - Fix .randomize_grouping to prevent collapsing of matrix when input in a single column. Changes in 1.5.7 - Add function .group_standards_iteration and .randomize_grouping to allow iteration through matrix of standards and group them if they are dissimilar enough. Changes in 1.5.6 - Fix issue in the vignette. Thanks @RemyDeB for the fix. Changes in 1.5.5 - Update objects to the new definitions in Spectra version 1.11.10. Changes in 1.5.4 - Add functions targetIndex and queryIndex to extract the indices of the matched pairs query-target. - Add examples and a section to the vignette explaining their use. Changes in 1.5.3 - Add support to matchValues for matching between data.frame and Spectra objects. Changes in 1.5.2 - Fix vignette, examples and unit tests using QFeatures. - Import query from AnnotationHub. Changes in 1.5.1 - Add possibility to select the spectra variable for retention time matching in matchSpectra (issue #98). Changes in version 1.3 Changes in 1.3.2 - Add mzR as suggested package to ensure package vignettes can be built. Changes in 1.3.1 - Small changes in matchSpectra to avoid unnecessary object creation. - Use backendBpparam to disable parallel processing of matchSpectra if the backend does not support it. Changes in version 1.1 Changes in 1.1.6 - scoreVariables function to return the names of the score variables in a Matched object. Changes in 1.1.5 - Fix issues on BioC build machines. Changes in 1.1.4 - matchSpectra: support a CompDb with parameter target. - Add CompAnnotionSource classes to support definition of references to annotation resources. - Add CompDbSource class defining a reference to a CompDb database. - matchSpectra: support for CompDbSource with parameter target. Changes in 1.1.3 - Extend filterMatches framework (issue #86). ScoreThresholdParam added to perform filtering the matches based on a threshold for the scores. Changes in 1.1.2 - lapply and endoapply methods (issue #84). lapply allows to apply any function to each subset of matches for each query element and returns the corresponding list of results. endoapply is similar but applies a function returning a Matched and returns a Matched representing updated matches. Changes in 1.1.1 - Extend filterMatches framework (issue #81). SelectMatchesParam and TopRankedMatchesParam added to perform respectively manual filtering and keeping only the best ranked matches for each query element. Changes in version 0.99 Changes in 0.99.15 - Highlight query and target spectra in different colors for validateMatchedSpectra. - query and/or target of type SummarizedExperiment supported for Matched objects. - MatchedSummarizedExperiment class removed. - query and/or target of type QFeatures supported for Matched objects. - Support SummarizedExperiment and QFeatures for both query and target parameters in matchValues. Changes in 0.99.14 - Improve plotly-based mirror plots in validateMatchedSpectra. Changes in 0.99.13 - Fix issue about matchedData not working for result objects of matchValues, Mz2MassParam and matchValues, Mz2MassRtParam (issue #69). Changes in 0.99.12 - Update plotly-based mirror plots in validateMatchedSpectra. Changes in 0.99.11 - Change matchMz into matchValues (issue #65). Changes in 0.99.10 - Add validateMatchedSpectra for manual inspection and validation of an MatchedSpectra object. Changes in 0.99.9 - Add setBackend for MatchedSpectra objects. Changes in 0.99.8 - Add matchMz, Mz2MassParam and matchMz, Mz2MassRtParam. (issue #56). Changes in 0.99.7 - Add formula matching functions. Changes in 0.99.5 - Add parameter ... to plotSpectraMirror. - Definitions of "score", "score_rt" changed to be the difference (with sign) between query and target m/z or retention time respectively. - "ppm_error" becomes error without sign. Changes in 0.99.4 - Add matches m/z error (variable "ppm_error") to the Matched object returned by matchMz. Changes in 0.99.3 - Address Herve's comments. Changes in version 0.2 Changes in 0.2.11 - Fix calculation of correct number of rows/columns of the plot in plotSpectraMirror. Changes in 0.2.10 - Add parameter toleranceRt to CompareSpectraParam to enable retention time-based pre-filtering (issue #35). Changes in 0.2.9 - Add support for manually defined adducts to Mass2MzParam (issue #41). Changes in 0.2.8 - Add parameter THRESHFUN_REVERSE to MatchForwardReverseParam to allow filtering results on forward and reverse score (issue #37). Changes in 0.2.7 - Performance improvement in matchSpectra if no precursor m/z filter is used (issue #38). - Report number of matching peaks in matchSpectra,MatchForwardReverseParam (issue #36). Changes in 0.2.6 - Fix bug in matchSpectra that was wrongly calculating the acceptable m/z difference if tolerance was > 0 (issue #34). Fix proposed by Hugo Varet (@hvaret). Changes in 0.2.5 - Improve performance of matchMz. - Rename queryColumn and targetColumn to queryColname and targetColname. Changes in 0.2.4 - Support data.frame, DataFrame and matrix in matchMz. - Add addMatches and filterMatches functions. Changes in 0.2.3 - Fixes in MatchedSpectra. Changes in 0.2.2 - Add MatchedSummarizedExperiment. Changes in 0.2.1 - Rename TargetMass2MzParam to Mass2MzParam. Changes in 0.2.0 - Add support for matching m/z against m/z and m/z in addition to retention times to matchMz. Changes in version 0.0 Changes in 0.0.4 - Fix vignette, documentations and unit tests.