NEWS.md

In jasenfinch/metabolyseR: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data

metabolyseR 0.15.4

• Fixed various tidyverse warnings.

• Fixed an error when calculating the mds dimensions for multiple class comparisons with differing numbers of observations.

• Added the transformPercent() method for the AnalysisData S4 class to scale as a percentage of feature maximum intensity.

• Feature intensities are now displayed as relative percent intensities in heat maps generated by plotExplanatoryHeatmap().

• Reduced the gap between the dendrogram and heat map in outputs of plotExplanatoryHeatmap().

metabolyseR 0.15.3

• Fixed the margin value displayed in plots from plotSupervisedRF()

• The plotExplanatoryHeatmap() method for the Analysis S4 class now returns a warning and skips plotting if an error is encountered whilst trying to plot a heat map.

metabolyseR 0.15.2

• Added the argument refactor to the method transformTICnorm() to enable the feature intensities of total ion count (TIC) normalised data to be refactored back to a range consistent with the original data by multiplying the normalised values by the median TIC.

• Removed the permutation cap when the perm argument of randomForest() is less than the total number of permutations possible.

metabolyseR 0.15.1

• The class occupancy methods now throw a helpful error message if no features are available on which to compute class occupancy.

• Fixed a bug where it was not possible to customize the order of class labels in the legend of plotLDA().

metabolyseR 0.15.0

• It is now possible to specify multiple cls arguments to the aggregation methods.

• Correlation thresholds are now available for both coefficient and total number using the minCoef and maxCor arguments in the correlations() method.

• Added the predictions() accessor method for the RandomForest S4 class to enable the retrieval of the out of bag model response predictions.

• The occupancy filtering methods now error if the value supplied to argument occupancy is non-numeric.

• Memory usage and performance improvements for the randomForest() method.

• Added type() and response() methods for the Univariate S4 class.

• plotLDA() now returns a warning and skips plotting if an error is encountered during PC-LDA.

• The value pre-treated is now the default for argument type in the Analysis S4 class accessor methods.

• Added the value argument to the explanatoryFeatures() method to allow the specification of on which importance value to apply the specified threshold.

• The specified cls argument is now correctly displayed on the x-axis title of the resulting plots from the plotFeature() method.

metabolyseR 0.14.10

• Added the method predict() for the RandomForest S4 class to predict model response values.

• Added the method mtry() for the AnalysisData S4 class to return the default mtry random forest parameter for a given response variable.

• Added the method tune() for the AnalysisData S4 class to tune the random forest parameters mtry and ntree for a given response variable.

metabolyseR 0.14.9

• Suppressed name repair console message encountered during random forest permutation testing.

• Added the proximity() method for extracting sample proximities from the RandomForest S4 class.

• Added the mds() method to perform multidimensional scaling on sample proximities from the RandomForest S4 class.

• Added the roc() method to calculate receiver-operator characteristic curves from the RandomForest S4 class.

metabolyseR 0.14.8

• An error is now thrown during random forest classification when less than two classes are specified.

• plotSupervisedRF() now skips plotting if errors are encountered during random forest training.

metabolyseR 0.14.7

• Single replicate classes now automatically removed by plotLDA().

metabolyseR 0.14.6

• plotExplanatoryHeatmap() method for the Analysis class now returns the plot only if the number of plots is equal to 1.

• Removed reference to the nCores parameter from the documentation example of metabolyse().

metabolyseR 0.14.5

• Correlation analysis results now include an absolute correlation coefficient column by which the results are also arranged in descending order.

metabolyseR 0.14.4

• Console output from imputeAll() now suppressed.

metabolyseR 0.14.3

• Temporarily added jasenfinch/missForest as a remote until stekhoven/missForest pull request #25 is resolved.

• The limit of the number of plotted features in plotExplanatoryHeatmap can now be specified using the featureLimit argument.

• plotExplanatoryHeatmap() now returns NULL and returns a message when no explanatory features are found.

• Fixed the alignment of the dendrogram branches with heat map rows in plotExplanatoryHeatmap().

• Fixed ggplot2::guides() warning in plotFeature() and plotTIC().

• Fixed bug in explanatoryFeatures() methods for Analysis class and lists where the threshold was not applied.

• Fixed the error in plotRSD() method for the Analysis class.

• Corrected the text in the modelling vignette concerning the results of using unsupervised random forest for outlier detection.

metabolyseR 0.14.2

• Package version, creation date and verbose argument added to prototype of Analysis class.

• All generics are now defined as standard generics.

• Added metrics method for Analysis class.

• metrics method for lists now ignores list elements that are not of class RandomForest.

metabolyseR 0.14.1

• Changed the RSDthresh argument default to 50% instead of 0.5% in QCrsdFilter generic.

metabolyseR 0.14.0

• Added a NEWS.md file to track changes to the package.

• pkgdown site now available at https://jasenfinch.github.io/metabolyseR/.

• Bug reports and issues URL at https://github.com/jasenfinch/metabolyseR/issues added to package DESCRIPTION.

• Dedicated vignettes now available for a quick start example analysis, data pre-treatment and data modelling.

• Function examples added to all documentation pages.

• Unit test coverage increased to > 95%.

• Parallel processing is now implemented using the future package.

• plan() from the future package is re-exported.

• RandomForest and Univariate classes now inherit from class the AnalysisData class.

• Improvements to plot theme aesthetics.

• type argument added to plotPCA(), plotLDA(), plotUnsupervisedRF() and plotSupervisedRF() methods for the Analysis class.

• "pre-treated" for specifying type argument in Analysis class methods now used over "preTreated"

• Added clsRename() method for renaming class information columns.

• plotMeasures() method renamed to plotMetrics().

• Added plotMDS(), plotImportance() and plotMetrics() methods for lists of RandomForest class objects.

• Added plotExplanatoryHeatmap() method for lists of RandomForest or Univariate class objects.

• Renamed keepVariables() and removeVariables() methods to keepFeatures() and removeFeatures().

• Added the helper functions preTreatmentElements(), preTreatmentMethods() and preTreatParameters() for declaring pre-treatment parameters for the AnalysisParameters class.

• Added the helper functions modellingMethods() and modellingParameters() for declaring modelling parameters for the AnalysisParameters class.

• Added helper function correlationsParameters() for declaring correlations parameters for the AnalysisParameters class.

• Added binaryComparisons() method for retrieving all possible binary class comparisons from an AnalysisData class object.

• changeParameter() now assigns parameter values through direct assignment.

• Added analysisResults() method from extracting analysis elements results from the Analysis class.

• Added exportParameters() method for exporting analysis parameters to YAML file format.

• Added dat() and sinfo() accessor methods for the Analysis class.

• Relative standard deviation (RSD) values are now specified and returned as percentages.

jasenfinch/metabolyseR documentation built on Sept. 18, 2023, 1:25 a.m.