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

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Documentation for package ‘ropls’ version 1.40.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

ropls-package	PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
aminoacids	Amino-Acids Dataset
cellulose	NIR-Viscosity example data set to illustrate multivariate calibration using PLS, spectral filtering and OPLS
checkW4M	Checking the consistency of a SummarizedExperiment or ExpressionSet instance with W4M format
checkW4M-method	Checking the consistency of a SummarizedExperiment or ExpressionSet instance with W4M format
coef-method	Coefficients method for (O)PLS models
coef.opls	Coefficients method for (O)PLS models
cornell	Octane of various blends of gasoline
fitted-method	Fitted method for 'opls' objects
fitted.opls	Fitted method for 'opls' objects
foods	Food consumption patterns accross European countries (FOODS)
fromW4M	fromW4M
getEset	getEset method
getEset,	getEset method
getEset-method	getEset method
getLoadingMN	getLoadingMN method for PCA/(O)PLS(-DA) models
getLoadingMN-method	getLoadingMN method for PCA/(O)PLS(-DA) models
getMset	getMset method
getMset,	getMset method
getMset-method	getMset method
getOpls	Getting the models from a SummarizedExperiment or a MultiAssayExperiment object
getOpls-method	Getting the models from a SummarizedExperiment or a MultiAssayExperiment object
getPcaVarVn	getPcaVarVn method for PCA models
getPcaVarVn-method	getPcaVarVn method for PCA models
getScoreMN	getScoreMN method for PCA/(O)PLS(-DA) models
getScoreMN-method	getScoreMN method for PCA/(O)PLS(-DA) models
getSubsetVi	getSubsetVi method for (O)PLS(-DA) models
getSubsetVi-method	getSubsetVi method for (O)PLS(-DA) models
getSummaryDF	getSummaryDF method for PCA/(O)PLS models
getSummaryDF-method	getSummaryDF method for PCA/(O)PLS models
getVipVn	getVipVn method for (O)PLS(-DA) models
getVipVn-method	getVipVn method for (O)PLS(-DA) models
getWeightMN	getWeightMN method for (O)PLS(-DA) models
getWeightMN-method	getWeightMN method for (O)PLS(-DA) models
imageF	view
linnerud	Linnerud Dataset
lowarp	A multi response optimization data set (LOWARP)
mark	'mark' Dataset
NCI60	Microarray gene expression profiles of the NCI 60 cell lines from 4 different platforms
opls	PCA, PLS(-DA), and OPLS(-DA)
opls-class	Class "opls"
opls-method	getEset method
opls-method	PCA, PLS(-DA), and OPLS(-DA)
oplsMultiDataSet-class	Class "oplsMultiDataSet"
oplsMultiDataSet-method	getMset method
plot-method	Plot Method for (O)PLS(-DA)
plot.opls	Plot Method for (O)PLS(-DA)
plot.oplsMultiDataSet	Plot Method for (O)PLS(-DA)
plot_score	PCA and (O)PLS(-DA) score plots
plot_score-method	PCA and (O)PLS(-DA) score plots
predict-method	Predict method for (O)PLS models
predict.opls	Predict method for (O)PLS models
print-method	Print method for 'opls' objects
print.opls	Print method for 'opls' objects
residuals	Residuals method for (O)PLS models
residuals-method	Residuals method for (O)PLS models
residuals.opls	Residuals method for (O)PLS models
ropls	PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
sacurine	Analysis of the human adult urinary metabolome variations with age, body mass index and gender
show-method	Show method for 'opls' objects
show.opls	Show method for 'opls' objects
strF	view
tested	Tested method for (O)PLS models
tested-method	Tested method for (O)PLS models
toW4M	Exporting a SummarizedExperiment or ExpressionSet instance into 3 tabulated files.
toW4M-method	Exporting a SummarizedExperiment or ExpressionSet instance into 3 tabulated files.
view	view
view-method	view