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

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).

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ropls")
AuthorEtienne A. Thevenot <etienne.thevenot@cea.fr>
Bioconductor views Classification Lipidomics MassSpectrometry Metabolomics PrincipalComponent Proteomics Regression Transcriptomics
Date of publicationNone
MaintainerEtienne A. Thevenot <etienne.thevenot@cea.fr>
LicenseCeCILL
Version1.8.0
http://dx.doi.org/10.1021/acs.jproteome.5b00354

View on Bioconductor

Functions

aminoacids Man page
cellulose Man page
checkW4M Man page
checkW4M,ExpressionSet-method Man page
coef.opls Man page
coef,opls-method Man page
cornell Man page
fitted.opls Man page
fitted,opls-method Man page
foods Man page
fromW4M Man page
getLoadingMN Man page
getLoadingMN,opls-method Man page
getPcaVarVn Man page
getPcaVarVn,opls-method Man page
getScoreMN Man page
getScoreMN,opls-method Man page
getSubsetVi Man page
getSubsetVi,opls-method Man page
getSummaryDF Man page
getSummaryDF,opls-method Man page
getVipVn Man page
getVipVn,opls-method Man page
getWeightMN Man page
getWeightMN,opls-method Man page
linnerud Man page
lowarp Man page
mark Man page
opls Man page
opls-class Man page
opls,data.frame-method Man page
opls,ExpressionSet-method Man page
opls,matrix-method Man page
plot.opls Man page
plot,opls-method Man page
predict.opls Man page
predict,opls-method Man page
print.opls Man page
print,opls-method Man page
residuals.opls Man page
residuals,opls-method Man page
ropls Man page
ropls-package Man page
sacurine Man page
show.opls Man page
show,opls-method Man page
strF Man page
tested Man page
tested,opls-method Man page
toW4M Man page
toW4M,ExpressionSet-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/allClasses.R R/allGenerics.R R/datasets.R R/functions.R R/helpers.R R/methods.R R/ropls-package.R
build
build/vignette.rds
data
data/aminoacids.csv.gz
data/cellulose.rdata
data/cornell.csv.gz
data/datalist
data/foods.csv.gz
data/linnerud.csv.gz
data/lowarp.csv.gz
data/mark.csv.gz
data/sacurine.rdata
inst
inst/CITATION
inst/doc
inst/doc/ropls-vignette.R
inst/doc/ropls-vignette.Rmd
inst/doc/ropls-vignette.pdf
inst/extdata
inst/extdata/sacurine_dataMatrix.tsv
inst/extdata/sacurine_sampleMetadata.tsv
inst/extdata/sacurine_variableMetadata.tsv
inst/unitTests
inst/unitTests/test_opls.R
man
man/aminoacids.Rd man/cellulose.Rd man/checkW4M.Rd man/coef.Rd man/cornell.Rd man/fitted.Rd man/foods.Rd man/fromW4M.Rd man/getLoadingMN.Rd man/getPcaVarVn.Rd man/getScoreMN.Rd man/getSubsetVi.Rd man/getSummaryDF.Rd man/getVipVn.Rd man/getWeightMN.Rd man/linnerud.Rd man/lowarp.Rd man/mark.Rd man/opls-class.Rd man/opls.Rd man/plot.Rd man/predict.Rd man/print.Rd man/residuals.Rd man/ropls-package.Rd man/sacurine.Rd man/show.Rd man/strF.Rd man/tested.Rd man/toW4M.Rd
tests
tests/runTests.R
vignettes
vignettes/ropls-vignette.Rmd
vignettes/ropls-vignette.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.