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 querySpectra with the index in the original object (issue #114).
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.
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.
