To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ropls")

In most cases, you don't need to download the package archive at all.

# ropls

This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see ropls.

## PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data

Bioconductor version: 3.3

Latent variable modeling with Principal Component Analysis (PCA) and Partial Least Squares (PLS) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. Orthogonal Partial Least Squares (OPLS) enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation. While performing similarly to PLS, OPLS facilitates interpretation. Successful applications of these chemometrics techniques include spectroscopic data such as Raman spectroscopy, nuclear magnetic resonance (NMR), mass spectrometry (MS) in metabolomics and proteomics, but also transcriptomics data. In addition to scores, loadings and weights plots, the package provides metrics and graphics to determine the optimal number of components (e.g. with the R2 and Q2 coefficients), check the validity of the model by permutation testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection or regression coefficients). The package can be accessed via a user interface on the Workflow4Metabolomics.org online resource for computational metabolomics (built upon the Galaxy environment).

Author: Etienne A. Thevenot <etienne.thevenot at cea.fr>

Maintainer: Etienne A. Thevenot <etienne.thevenot at cea.fr>

Citation (from within R, enter citation("ropls")):

### Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ropls")

### Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ropls")

 PDF R Script PCA, PLS and OPLS with \emph{ropls} PDF Reference Manual Text NEWS

### Details

 biocViews Classification, Lipidomics, MassSpectrometry, Metabolomics, PrincipalComponent, Proteomics, Regression, Software, Transcriptomics Version 1.4.6 In Bioconductor since BioC 3.2 (R-3.2) (1 year) License CeCILL Depends methods Imports LinkingTo Suggests RUnit, BiocGenerics, BiocStyle, faahKO, xcms, CAMERA SystemRequirements Enhances URL http://dx.doi.org/10.1021/acs.jproteome.5b00354 Depends On Me biosigner Imports Me Suggests Me Build Report

### Package Archives

Follow Installation instructions to use this package in your R session.

 Package Source ropls_1.4.6.tar.gz Windows Binary ropls_1.4.6.zip Mac OS X 10.9 (Mavericks) ropls_1.4.6.tgz Subversion source (username/password: readonly) Git source https://github.com/Bioconductor-mirror/ropls/tree/release-3.3 Package Short Url http://bioconductor.org/packages/ropls/ Package Downloads Report Download Stats

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