NEWS.md

In EuracBiomedicalResearch/CompMetaboTools: Utility Functions from the Eurac Research Computational Metabolomics Team

CompMetaboTools 0.4

CompMetaboTools 0.4.4

• Remove rsd and rowRsd (have been transferred to MetaboCoreUtils).

CompMetaboTools 0.4.3

• Add averageSE function to average replicates in a SummarizedExperiment.

CompMetaboTools 0.4.2

• Pass ... also to the plot call in plot_pca.

CompMetaboTools 0.4.1

• Remove plotOverlay function (replaced by plotChromatogramsOverlay from xcms.

CompMetaboTools 0.4.0

• Remove all feature grouping code (added to xcms).

CompMetaboTools 0.3

CompMetaboTools 0.3.3

• Add parameter type to chromPeakArea.

CompMetaboTools 0.3.2

• Add chromPeakArea function.
• Add groupFeatures,XCMSnExp,AbundanceSimilarityParam.

CompMetaboTools 0.3.1

• Add groupFeatures,XCMSnExp,SimilarRtimeParam.

CompMetaboTools 0.3.0

• Move groupClosest and groupSimilarityMatrix to the MsFeatures package.

CompMetaboTools 0.2

CompMetaboTools 0.2.5

• Add parameter mad to rsd and rowRsd allowing to base the RSD calculation on the median absolute deviation instead of the standard deviation.

CompMetaboTools 0.2.4

• Add moreAreValidThan to test for proportion of non-missing values in rows of a matrix.

CompMetaboTools 0.2.3

• Add joyPlot to plot stacked (partially overlapping) chromatograms.

CompMetaboTools 0.2.2

• Remove the extractSpectraData function as it was added to MSnbase.

CompMetaboTools 0.1

CompMetaboTools 0.1.0

• Change from Chromatograms to MChromatograms and from Spectra to MSpectra following the changes introduced in MSnbase 2.15.3.

CompMetaboTools 0.0.8

• Fix issue in .group_correlation_matrix that would not group elements even if their correlation is larger than the threshold in some special cases.
• Add featureGroupSpectra function to extract a spectrum for each feature group which can be either a pseudo spectrum or a full scan MS1 spectrum.

CompMetaboTools 0.0.7

• Add matchRtMz function to match features based on retention time and m/z values.
• Fix groupFeatures for older xcms result objects that don't record MS level.
• Add plotFeatureGroups to draw feature groups into the m/z-rt space.

CompMetaboTools 0.0.6

• Add the plotOverlay function to create a overlay plot of EICs.
• Use a less greedy grouping algorithm: create only groups of features with a correlation between each other >= threshold.
• groupFeatures adds a process history step to the XCMSnExp with the parameter object.
• Add AbundanceCorrelationParam method to group features based on feature abundances.
• Add groupFeatures method for XCMSnExp objects allowing to group features.
• Add SimilarRtimeParam and EicCorrelationParam feature grouping methods.

CompMetaboTools 0.0.5

• Add groupClosest function to group values into small groups based on values being smaller than a threshold.
• Add groupToSinglePolarityPairs function.
• Add c method to (row-wise) combine Chromatograms objects.
• Add groupByCorrelation to allow grouping of rows within a numeric matrix by pairwise correlation with each other.
• Add groupEicCorrelation to allow grouping of (extracted ion) chromatograms (EICs) based on pairwise correlation.

CompMetaboTools 0.0.4

• Add extractSpectraData to support converting data from the MSnbase to the new Spectra package.

CompMetaboTools 0.0.2

• Add withinBatchFit, withinBatchAdjust and dropModels function to perform per-batch separate model-based adjustments.

CompMetaboTools 0.0.2

• Add flag_* functions to flag/identify potentially problematic model fits e.g. fitted to experimental data to explain an injection-order-dependent signal drift.

CompMetaboTools 0.0.1

• Add extract_time_stamp.
• Add plot_pca.
• Add rsd and rowRsd.
• Add sync_files_local and remove_local_files.

EuracBiomedicalResearch/CompMetaboTools documentation built on Jan. 31, 2024, 1:14 p.m.