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Bioconductor - ropls

ropls

This is the released version of ropls; for the devel version, see ropls.

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

Bioconductor version: Release (3.21)

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 [aut, cre] ORCID: 0000-0003-1019-4577

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

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ropls")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("ropls")

Details biocViews Classification, ImmunoOncology, Lipidomics, MassSpectrometry, Metabolomics, PrincipalComponent, Proteomics, Regression, Software, Transcriptomics Version 1.40.0 In Bioconductor since BioC 3.2 (R-3.2) (9.5 years) License CeCILL Depends R (>= 3.5.0) Imports Biobase, ggplot2, graphics, grDevices, methods, plotly, stats, MultiAssayExperiment, MultiDataSet, SummarizedExperiment, utils System Requirements URL https://doi.org/10.1021/acs.jproteome.5b00354 See More Suggests BiocGenerics, BiocStyle, knitr, multtest, omicade4, phenomis, rmarkdown, testthat Linking To Enhances Depends On Me Imports Me ASICS, biosigner, lipidr, MultiBaC, phenomis Suggests Me autonomics, ptairMS, structToolbox, MetabolomicsBasics Links To Me Build Report Build Report Package Archives

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

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