NEWS

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MetaboAnnotation 1.15

Changes in 1.15.3

• Use Spectra::rbindlistWithRownames() to expand on the changes introduced in version 1.15.2 supporting also data.frames with row names.

Changes in 1.15.2

• Use data.table::rbindlist() for merging lists of data.frame's to improve performance.

Changes in 1.15.1

• Remove dependency on the msdata package: get test data from MsDataHub.

MetaboAnnotation 1.13

Changes in 1.13.3

• Expand documentation for CompareSpectraParam to also mention use of msentropy or GNPS-like similarity calculation.

Changes in 1.13.2

• For plotSpectraMirror,MatchedSpectra method, we now pass the available ppm and tolerance value that were used in the creation of the object.

Changes in 1.13.1

• Add parameter matchedPeaksCount to CompareSpectraParam that enables reporting of the number of matched peaks for matchSpectra() with CompareSpectraParam. The result are reported in a column "matched_peaks_count".

MetaboAnnotation 1.11

Changes in 1.11.1

• Fix reporting of matched peaks with MatchForwardReverseParam and gnps-matching/similarity calculation (issue #119).

MetaboAnnotation 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.

MetaboAnnotation 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.

MetaboAnnotation 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).

MetaboAnnotation 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.

MetaboAnnotation 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.

MetaboAnnotation 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.

MetaboAnnotation 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.

MetaboAnnotation 0.0

Changes in 0.0.4

• Fix vignette, documentations and unit tests.