Package: ropls
Type: Package
Title: PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and
        feature selection of omics data
Version: 1.6.2
Date: 2016-11-01
Author: Etienne A. Thevenot <etienne.thevenot@cea.fr>
Maintainer: Etienne A. Thevenot <etienne.thevenot@cea.fr>
biocViews: Regression, Classification, PrincipalComponent,
        Transcriptomics, Proteomics, Metabolomics, Lipidomics,
        MassSpectrometry
Description: 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).
Imports: Biobase, methods
Suggests: BiocGenerics, BiocStyle, CAMERA, faahKO, knitr, multtest,
        rmarkdown, RUnit, xcms
VignetteBuilder: knitr
License: CeCILL
Lazy data: yes
URL: http://dx.doi.org/10.1021/acs.jproteome.5b00354
NeedsCompilation: no
RoxygenNote: 5.0.1
Packaged: 2016-11-02 00:11:13 UTC; biocbuild
Built: R 3.3.1; ; 2016-11-02 04:27:25 UTC; windows
