RFmarkerDetector: Multivariate Analysis of Metabolomics Data using Random Forests

Share:

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 <piergiorgio.palla@diee.unica.it>
License
GPL-3
Version
1.0.1

View on CRAN

Man pages

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
simpleData
simpleData
tuneMTRY
Tuning of the mtry parameter for a Random Forest model
tuneNTREE
Tuning of the ntree parameter (i.e. the number of trees) for...

Files in this package

RFmarkerDetector
RFmarkerDetector/NAMESPACE
RFmarkerDetector/data
RFmarkerDetector/data/simpleData.rda
RFmarkerDetector/data/cachexiaData.rda
RFmarkerDetector/R
RFmarkerDetector/R/scaling.R
RFmarkerDetector/R/RFTuning.R
RFmarkerDetector/R/exampleData.R
RFmarkerDetector/R/RFMCcv.R
RFmarkerDetector/R/filtering.R
RFmarkerDetector/R/CombinatorialCV.R
RFmarkerDetector/R/plotMethods.R
RFmarkerDetector/R/Exploring.R
RFmarkerDetector/R/BiomarkerDiscovery.R
RFmarkerDetector/MD5
RFmarkerDetector/DESCRIPTION
RFmarkerDetector/man
RFmarkerDetector/man/aucMCV.Rd
RFmarkerDetector/man/forestPerformance.Rd
RFmarkerDetector/man/optimizeMTRY.Rd
RFmarkerDetector/man/plot.pca.loadings.Rd
RFmarkerDetector/man/mccv.Rd
RFmarkerDetector/man/autoscale.Rd
RFmarkerDetector/man/rfMCCV.Rd
RFmarkerDetector/man/paretoscale.Rd
RFmarkerDetector/man/rfMCCVPerf.Rd
RFmarkerDetector/man/meanCenter.Rd
RFmarkerDetector/man/screeplot.Rd
RFmarkerDetector/man/lqvarFilter.Rd
RFmarkerDetector/man/plot.pca.scores.Rd
RFmarkerDetector/man/tuneMTRY.Rd
RFmarkerDetector/man/getBestRFModel.Rd
RFmarkerDetector/man/plot.mccv.Rd
RFmarkerDetector/man/rsd.Rd
RFmarkerDetector/man/rsdFilter.Rd
RFmarkerDetector/man/plot.mds.Rd
RFmarkerDetector/man/simpleData.Rd
RFmarkerDetector/man/mds.Rd
RFmarkerDetector/man/cachexiaData.Rd
RFmarkerDetector/man/combinatorialRFMCCV.Rd
RFmarkerDetector/man/pca.Rd
RFmarkerDetector/man/plotAUCvsCombinations.Rd
RFmarkerDetector/man/plotVarFreq.Rd
RFmarkerDetector/man/tuneNTREE.Rd
RFmarkerDetector/man/plotOOBvsMTRY.Rd
RFmarkerDetector/man/getAvgAUC.Rd