NEWS.md
In rformassspectrometry/MetaboAnnotation: Utilities for Annotation of Metabolomics Data

MetaboAnnotation 1.9

Fix missing ProtGenerics dependency.

Add parameter scalePeaks to plotSpectraMirror to allow scaling peak intensities before plotting.

MetaboAnnotation 1.7

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).

Import setBackend() generic from ProtGenerics.

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.

Update the Spectra objects within the package to the new versions.

Add examples and a section to the vignette explaining the use of createStandardMixes.

MetaboAnnotation 1.5

Addition of global function createStandardMixes.

Fix .randomize_grouping to prevent collapsing of matrix when input in a single column.

Add function .group_standards_iteration and .randomize_grouping to allow iteration through matrix of standards and group them if they are dissimilar enough.

Fix issue in the vignette. Thanks @RemyDeB for the fix.

Update objects to the new definitions in Spectra version 1.11.10.

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.

Add support to matchValues for matching between data.frame and Spectra objects.

Fix vignette, examples and unit tests using QFeatures.
Import query from AnnotationHub.

Add possibility to select the spectra variable for retention time matching in matchSpectra (issue #98).

MetaboAnnotation 1.3

Add mzR as suggested package to ensure package vignettes can be built.

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

scoreVariables function to return the names of the score variables in a Matched object.

Fix issues on BioC build machines.

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.

Extend filterMatches framework (issue #86). ScoreThresholdParam added to perform filtering the matches based on a threshold for the scores.

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.

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

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.

Improve plotly-based mirror plots in validateMatchedSpectra.

Fix issue about matchedData not working for result objects of matchValues, Mz2MassParam and matchValues, Mz2MassRtParam (issue #69).

Update plotly-based mirror plots in validateMatchedSpectra.

Change matchMz into matchValues (issue #65).

Add validateMatchedSpectra for manual inspection and validation of an MatchedSpectra object.

Add setBackend for MatchedSpectra objects.

Add matchMz, Mz2MassParam and matchMz, Mz2MassRtParam. (issue #56).

Add formula matching functions.

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.

Add matches m/z error (variable "ppm_error") to the Matched object returned by matchMz.

Address Herve's comments.

MetaboAnnotation 0.2

Fix calculation of correct number of rows/columns of the plot in plotSpectraMirror.

Add parameter toleranceRt to CompareSpectraParam to enable retention time-based pre-filtering (issue #35).

Add support for manually defined adducts to Mass2MzParam (issue #41).

Add parameter THRESHFUN_REVERSE to MatchForwardReverseParam to allow filtering results on forward and reverse score (issue #37).

Performance improvement in matchSpectra if no precursor m/z filter is used (issue #38).
Report number of matching peaks in matchSpectra,MatchForwardReverseParam (issue #36).

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).

Improve performance of matchMz.
Rename queryColumn and targetColumn to queryColname and targetColname.

Support data.frame, DataFrame and matrix in matchMz.
Add addMatches and filterMatches functions.

Fixes in MatchedSpectra.

Add MatchedSummarizedExperiment.

Rename TargetMass2MzParam to Mass2MzParam.

Add support for matching m/z against m/z and m/z in addition to retention times to matchMz.

MetaboAnnotation 0.0

Fix vignette, documentations and unit tests.

rformassspectrometry/MetaboAnnotation documentation built on Oct. 20, 2024, 7:25 p.m.

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