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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.