Man pages for hdsu-bioquant/ButchR
Non-Negative Matrix Factorization Suite
| amariDistance | Compute amari type distance between two matrices |
| auc | Helper function to estimate AUC in the recovery plots |
| ButchR_integrativeNMF-class | Integrative NMF Class |
| ButchR_joinNMF-class | Join NMF Class |
| ButchR_NMF-class | The ButchR_NMF class |
| compute_OptKStats_NMF | Computes factorization optimal K stats |
| compute_SignatureFeatures-methods | Compute Signature Features Performs feature extraction for... |
| cosineDissMat | Create distance matrix with cosine similarity with matrix... |
| FrobError-methods | Frobenius error for all factorization ranks |
| generateRiverplot-methods | NMF riverplot |
| gg_plotKStats | Plots optimal K metrics |
| HMatrix-methods | H-Matrix (H-Matrix with smallest frobError) |
| iNMF_lambda_tuning | Integrative NMF Tune Lambda |
| leukemia | Microarray expression data of B-ALL, T-ALL and AML samples. |
| nnls_sol | Find non-negative exposures of one matrix in another matrix |
| normalizeH-methods | Normalize the signatures matrix (H) |
| normalize_matrix_per_dim | Normalize matrix by columns |
| normalizeUpperQuartile | Function to normalizeUpperQuartile on a matrix |
| normalizeW-methods | Normalize the signatures matrix (W) |
| OptK-ButchR_NMF-method | Return optimal K |
| OptK-methods | Return optimal K |
| OptKStats-ButchR_NMF-method | Return optimal factorization rank (K) Statistics |
| OptKStats-methods | Return optimal factorization rank (K) Statistics |
| orderBinary | Function to order binary data matrix |
| rankTransform | Function to rankTransforma matrix |
| recovery_plot-methods | Recovery plot |
| regularizeH-methods | Regularize the signatures matrix (H) |
| relabelRiverplot | Relabel and recolour a riverplot |
| reorderEdges | Order the riverplot edges to prevent crossings from a single... |
| run_iNMF_tensor | Integrative NMF |
| run_joinNMF_tensor | Join NMF |
| run_NMF_tensor | Single view NMF |
| sigmoidTransform | Function to used to perform a k-means k=2 on a W matrix |
| sigmoidTransform2 | Function to used to perform a k-means k=2 on a W matrix -... |
| SignatureFeatures-methods | Signature Features |
| SignatureSpecificFeatures-methods | Signature Specific Features |
| source_NMFtensor_function | Single view NMF implementations |
| val_graph_GRNMF_SC | Validate if input graph is a matrix for GRNMF_SC |
| val_nonnegative_matrix | Validate if input matrix for NMF |
| val_positive_numeric | Validate input positive numeric vector |
| val_ranks_torun | Validate input ranks |
| val_single_boolean | Validate input single boolean |
| val_single_integer | Validate input single numeric integer |
| val_single_numeric | Validate input single numeric |
| WcomputeFeatureStats | Computes Signature specific features |
| WMatrix-methods | W-Matrix (W-Matrix with smallest frobError) |
| yNodeCoords | Order the riverplot nodes to minimize crossings |
