Omics Data Integration Project

auroc | Area Under the Curve (AUC) and Receiver Operating... |

background.predict | Calculate prediction areas |

biplot | biplot methods for 'pca' family |

block.pls | N-integration with Projection to Latent Structures models... |

block.plsda | N-integration with Projection to Latent Structures models... |

block.spls | N-integration and feature selection with sparse Projection to... |

block.splsda | N-integration and feature selection with Projection to Latent... |

breast.TCGA | Breast Cancer multi omics data from TCGA |

breast.tumors | Human Breast Tumors Data |

cim | Clustered Image Maps (CIMs) ("heat maps") |

cimDiablo | Clustered Image Maps (CIMs) ("heat maps") for DIABLO |

circosPlot | circosPlot for DIABLO |

colors | Color Palette for mixOmics |

diverse.16S | 16S microbiome data: most diverse bodysites from HMP |

explained_variance | Calculation of explained variance |

get.confusion_matrix | Create confusion table and calculate the Balanced Error Rate |

image.tune.rcc | Plot the cross-validation score. |

imgCor | Image Maps of Correlation Matrices between two Data Sets |

ipca | Independent Principal Component Analysis |

Koren.16S | 16S microbiome atherosclerosis study |

linnerud | Linnerud Dataset |

liver.toxicity | Liver Toxicity Data |

logratio-transformations | Log-ratio transformation |

map | Classification given Probabilities |

mat.rank | Matrix Rank |

mint.block.pls | NP-integration |

mint.block.plsda | NP-integration with Discriminant Analysis |

mint.block.spls | NP-integration for integration with variable selection |

mint.block.splsda | NP-integration with Discriminant Analysis and variable... |

mint.pca | P-integration with Principal Component Analysis |

mint.pls | P-integration |

mint.plsda | P-integration with Projection to Latent Structures models... |

mint.spls | P-integration with variable selection |

mint.splsda | P-integration with Discriminant Analysis and variable... |

mixOmics | PLS-derived methods: one function to rule them all! |

multidrug | Multidrug Resistence Data |

nearZeroVar | Identification of zero- or near-zero variance predictors |

network | Relevance Network for (r)CCA and (s)PLS regression |

nipals | Non-linear Iterative Partial Least Squares (NIPALS) algorithm |

nutrimouse | Nutrimouse Dataset |

pca | Principal Components Analysis |

perf | Compute evaluation criteria for PLS, sPLS, PLS-DA, sPLS-DA,... |

plotArrow | Arrow sample plot |

plotDiablo | Graphical output for the DIABLO framework |

plotIndiv | Plot of Individuals (Experimental Units) |

plotLoadings | Plot of Loading vectors |

plot.pca | Show PCA output |

plot.perf | Plot for model performance |

plot.rcc | Canonical Correlations Plot |

plot.spca | Show sPCA output |

plot.tune | Plot for model performance |

plotVar | Plot of Variables |

pls | Partial Least Squares (PLS) Regression |

plsda | Partial Least Squares Discriminant Analysis (PLS-DA). |

predict | Predict Method for (mint).(block).(s)pls(da) methods |

rcc | Regularized Canonical Correlation Analysis |

S3methods-print | Print Methods for CCA, (s)PLS, PCA and Summary objects |

selectVar | Output of selected variables |

sipca | Independent Principal Component Analysis |

spca | Sparse Principal Components Analysis |

spls | Sparse Partial Least Squares (sPLS) |

splsda | Sparse Partial Least Squares Discriminant Analysis (sPLS-DA) |

srbct | Small version of the small round blue cell tumors of... |

stemcells | Human Stem Cells Data |

study_split | divides a data matrix in a list of matrices defined by a... |

summary | Summary Methods for CCA and PLS objects |

tune | Generic function to choose the parameters in the different... |

tune.block.splsda | Tuning function for block.splsda method (N-integration with... |

tune.mint.splsda | Estimate the parameters of mint.splsda method |

tune.pca | Tune the number of principal components in PCA |

tune.rcc | Estimate the parameters of regularization for Regularized CCA |

tune.spls | Tuning functions for sPLS method |

tune.splsda | Tuning functions for sPLS-DA method |

tune.splslevel | Tuning functions for multilevel sPLS method |

unmap | Dummy matrix for an outcome factor |

vac18 | Vaccine study Data |

vac18.simulated | Simulated data based on the vac18 study for multilevel... |

vip | Variable Importance in the Projection (VIP) |

withinVariation | Within matrix decomposition for repeated measurements... |

wrapper.rgcca | mixOmics wrapper for Regularised Generalised Canonical... |

wrapper.sgcca | mixOmics wrapper for Sparse Generalised Canonical Correlation... |

yeast | Yeast metabolomic study |

zz-defunct | Estimate the parameters of regularization for Regularized CCA |

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