RFmarkerDetector: Multivariate Analysis of Metabolomics Data using Random Forests
Version 1.0.1

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.

Browse man pages Browse package API and functions Browse package files

AuthorPiergiorgio Palla, Giuliano Armano
Date of publication2016-02-29 01:29:57
MaintainerPiergiorgio Palla <piergiorgio.palla@diee.unica.it>
LicenseGPL-3
Version1.0.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RFmarkerDetector")

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...

Functions

aucMCV Man page Source code
autoscale Man page Source code
cachexiaData Man page
combinatorialRFMCCV Man page Source code
forestPerformance Man page Source code
getAvgAUC Man page Source code
getBestRFModel Man page Source code
lqvarFilter Man page Source code
mccv Man page Source code
mds Man page Source code
meanCenter Man page Source code
optimizeMTRY Man page Source code
paretoscale Man page Source code
pca Man page Source code
plot.mccv Man page Source code
plot.mds Man page Source code
plot.pca.loadings Man page Source code
plot.pca.scores Man page Source code
plotAUCvsCombinations Man page Source code
plotOOBvsMTRY Man page Source code
plotVarFreq Man page Source code
rfMCCV Man page Source code
rfMCCVPerf Man page Source code
rsd Man page Source code
rsdFilter Man page Source code
screeplot Man page Source code
simpleData Man page
tuneMTRY Man page Source code
tuneNTREE Man page Source code

Files

NAMESPACE
data
data/simpleData.rda
data/cachexiaData.rda
R
R/scaling.R
R/RFTuning.R
R/exampleData.R
R/RFMCcv.R
R/filtering.R
R/CombinatorialCV.R
R/plotMethods.R
R/Exploring.R
R/BiomarkerDiscovery.R
MD5
DESCRIPTION
man
man/aucMCV.Rd
man/forestPerformance.Rd
man/optimizeMTRY.Rd
man/plot.pca.loadings.Rd
man/mccv.Rd
man/autoscale.Rd
man/rfMCCV.Rd
man/paretoscale.Rd
man/rfMCCVPerf.Rd
man/meanCenter.Rd
man/screeplot.Rd
man/lqvarFilter.Rd
man/plot.pca.scores.Rd
man/tuneMTRY.Rd
man/getBestRFModel.Rd
man/plot.mccv.Rd
man/rsd.Rd
man/rsdFilter.Rd
man/plot.mds.Rd
man/simpleData.Rd
man/mds.Rd
man/cachexiaData.Rd
man/combinatorialRFMCCV.Rd
man/pca.Rd
man/plotAUCvsCombinations.Rd
man/plotVarFreq.Rd
man/tuneNTREE.Rd
man/plotOOBvsMTRY.Rd
man/getAvgAUC.Rd
RFmarkerDetector documentation built on May 20, 2017, 5:22 a.m.