A collection of tools for multivariate analysis of metabolomics data, which includes several preprocessing methods (normalization, scaling) and various exploration and data visualization techniques (Principal Components Analysis and Multi Dimensional Scaling). The core of the package is the Random Forest algorithm used for the construction, optimization and validation of classification models with the aim of identifying potentially relevant biomarkers.
|Author||Piergiorgio Palla, Giuliano Armano|
|Date of publication||2016-02-29 01:29:57|
|Maintainer||Piergiorgio Palla <email@example.com>|
aucMCV: AUC multiple cross-validation
autoscale: Unit variance scaling method performed on the columns of the...
cachexiaData: Metabolite concentrations
combinatorialRFMCCV: Combinatorial Monte Carlo CV
forestPerformance: Characterizing the performance of a Random Forest model
getAvgAUC: Computing the average AUC
getBestRFModel: Extracting the best performing Random Forest model
lqvarFilter: Filtering 'low quality' variables from the original dataset
mccv: mccv class
mds: mds class
meanCenter: Mean centering performed on the columns of the data (i.e....
optimizeMTRY: Mtry Optimization
paretoscale: Pareto scaling method performed on the columns of the data...
pca: Principal Component Analysis
plotAUCvsCombinations: Plotting the average AUC as a function of the number of...
plot.mccv: Plotting single or multiple ROC curves of the cross-validated...
plot.mds: Multi-dimensional Scaling (MDS) Plot
plotOOBvsMTRY: Plotting the average OOB error and its 95% confidence...
plot.pca.loadings: PCA Loadings plot This function plots the relation between...
plot.pca.scores: PCA Scores plot This function creates a plot that graphically...
plotVarFreq: Variable Frequency Plot
rfMCCV: Monte Carlo cross-validation of Random Forest models
rfMCCVPerf: Extracting average accuracy and recall of a list of Random...
rsd: Computing relative standard deviation of a vector
rsdFilter: Filtering less informative variables
screeplot: Scree Plot
tuneMTRY: Tuning of the mtry parameter for a Random Forest model
tuneNTREE: Tuning of the ntree parameter (i.e. the number of trees) for...