Changes in version 1.10
Changes in 1.10.1
- Fix reporting of matched peaks with MatchForwardReverseParam and
gnps-matching/similarity calculation (issue #119).
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.