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

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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@cea.fr>
Date of publication
None
Maintainer
Etienne A. Thevenot <etienne.thevenot@cea.fr>
License
CeCILL
Version
1.6.2
URLs

View on Bioconductor

Man pages

aminoacids
Amino-Acids Dataset
cellulose
NIR-Viscosity example data set to illustrate multivariate...
checkW4M
Checking the consistency of an ExpressionSet instance with...
coef
Coefficients method for (O)PLS models
cornell
Octane of various blends of gasoline
fitted
Fitted method for 'opls' objects
foods
Food consumption patterns accross European countries (FOODS)
fromW4M
fromW4M
getLoadingMN
getLoadingMN method for PCA/(O)PLS(-DA) models
getPcaVarVn
getPcaVarVn method for PCA models
getScoreMN
getScoreMN method for PCA/(O)PLS(-DA) models
getSubsetVi
getSubsetVi method for (O)PLS(-DA) models
getSummaryDF
getSummaryDF method for PCA/(O)PLS models
getVipVn
getVipVn method for (O)PLS(-DA) models
getWeightMN
getWeightMN method for (O)PLS(-DA) models
linnerud
Linnerud Dataset
lowarp
A multi response optimization data set (LOWARP)
mark
'mark' Dataset
opls
PCA, PLS(-DA), and OPLS(-DA)
opls-class
Class "opls"
plot
Plot Method for (O)PLS(-DA)
predict
Predict method for (O)PLS models
print
Print method for 'opls' objects
residuals
Residuals method for (O)PLS models
ropls-package
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and...
sacurine
Analysis of the human adult urinary metabolome variations...
show
Show method for 'opls' objects
strF
Printed summary of an R object
tested
Tested method for (O)PLS models
toW4M
Exporting ExpressionSet instance into 3 tabulated files.

Files in this package

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