Man pages for agapow/subtypr
Robust and Validated Patient Subtyping for Precision Medicine
| adjusted_rand_index | Adjusted rand index |
| analyze_survival | Plots the survival curves and compute the Cox p-value |
| breast_cancer_data | Breast cancer multi-omics data |
| check_distribution | Plot the distribution of the features |
| consensus_spectral_clustering | Apply consensus clustering on affinity matrix. |
| dunn_index | Dunn index |
| entropy | Return entropy of vector |
| evaluation | Evaluate parameters |
| flag_data | Simple quality control on sample-feature matrices |
| gbm_data | Glioblastoma multiforme (GBM) multi-omics data |
| generate_multi_moclust | Generate simulated data |
| generate_multi_structured | Generate synthetic data based on a list of features matrics. |
| generate_multi_unstructured | Generate a list of synthetic data matrices for validation |
| generate_partitions | Generate a partitions matrix |
| generate_single_moclust | Generate simulated data |
| generate_synth_data | Generate 'multi-omic' synthetic data matrices for validation |
| get_method | Load built-in methods |
| get_metric | Load built-in metrics |
| hello | Hello, World! |
| homogeneity_completeness_vmeasure | Homogeneity, completeness and V-Measure metrics for partition... |
| meila_vi | Meila's variation of information index |
| metrics_list | Metrics implemented |
| mutual_information | Calculate mutual information of two vectors |
| normalized_mutual_information | Normalized mutual information |
| overview_metrics | An overview of the results with all available metrics |
| plot_affinity_matrix | Plot clustered affinity matrix |
| plot_clinical_features | Box-plot of clinical features for a given partition of the... |
| pre_process | Pre-process feature matrices before analysis. |
| select_features | Selection of important features |
| select_mad | Mean Absolute Deviation (MAD) cutoff |
| select_pca | Apply principal components analysis |
| select_variance | Variance cutoff |
| silhouette_affinity | Silhouette index for affinity matrix |
| silhouette_distance | Classic silhouette index for distance matrix |
| sparse_methylation | Sparse data to test tools |
| subtype_anf | Subtypes using Affinity Network Fusion |
| subtype_pins | Subtypes using PINSPlus package |
| subtype_snf | Subtypes patients using Similarity Network Fusion |
| tuning | Tunes the methods to have the best set of parameters |
