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

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ropls

DOI: 10.18129/B9.bioc.ropls    

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

Bioconductor version: Release (3.5)

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 Vignette Title
PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, Lipidomics, MassSpectrometry, Metabolomics, PrincipalComponent, Proteomics, Regression, Software, Transcriptomics
Version 1.8.0
In Bioconductor since BioC 3.2 (R-3.2) (2 years)
License CeCILL
Depends
Imports Biobase, methods
LinkingTo
Suggests BiocGenerics, BiocStyle, CAMERA, faahKO, knitr, multtest, rmarkdown, RUnit, xcms
SystemRequirements
Enhances
URL http://dx.doi.org/10.1021/acs.jproteome.5b00354
Depends On Me
Imports Me biosigner, proFIA, rqt
Suggests Me
Build Report  

Package Archives

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

Package Source ropls_1.8.0.tar.gz
Windows Binary ropls_1.8.0.zip
Mac OS X 10.11 (El Capitan) ropls_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ropls
Package Short Url http://bioconductor.org/packages/ropls/
Package Downloads Report Download Stats

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