Package: mixOmics 6.37.0

Preamble | Introduction | Input data | Methods | Some background knowledge | Overview | Key publications | Outline of this Vignette | Other methods not covered in this vignette | Let's get started | Installation | Load the package | Upload data | Quick start in mixOmics | PCA on the multidrug study | Load the data | Example: PCA | Choose the number of components | PCA with fewer components | Identify the informative variables | Sample plots | Variable plot: correlation circle plot | Biplot: samples and variables | Example: sparse PCA | Choose the number of variables to select | Final sparse PCA | Sample and variable plots | PLS on the liver toxicity study | Load the data | Example: sPLS1 regression | Number of dimensions using the $Q^2$ criterion | Number of variables to select in $\boldsymbol X$ | Final sPLS1 model | Sample plots | Performance assessment of sPLS1 | Example: PLS2 regression | Number of dimensions using the $Q^2$ criterion | Number of variables to select in both $\boldsymbol X$ and $\boldsymbol Y$ | Final sPLS2 model | Numerical outputs | Importance variables | Graphical outputs | Performance | PLS-DA on the SRBCT case study | Load the data | Example: PLS-DA | Initial exploration with PCA | Number of components in PLS-DA | Final PLS-DA model | Classification performance | Background prediction | Example: sPLS-DA | Number of variables to select | Final model and performance | Variable selection and stability | Sample visualisation | Variable visualisation | Take a detour: prediction | AUROC outputs complement performance evaluation | N-Integration | Block sPLS-DA on the TCGA case study | Load the data | Parameter choice | Design matrix | Number of components | Number of variables to select | Final model | Sample plots | plotDiablo | plotIndiv | plotArrow | Variable plots | plotVar | circosPlot | network | plotLoadings | cimDiablo | Model performance and prediction | P-Integration | MINT on the stem cell case study | Load the data | Example: MINT PLS-DA | Example: MINT sPLS-DA | Number of variables to select | Final MINT sPLS-DA model | Sample plots | Variable plots | Correlation circle plot | Clustered Image Maps | Relevance networks | Variable selection and loading plots | Classification performance | Take a detour | AUC | Prediction on an external study | Session Information | mixOmics version | Session info | References