Man pages for markgene/yamatClassifier
Yet Another Methylation Array Toolkit: Classifier
| compute_relative_log_expression | Computing relative log expression |
| cor_mtest | Computing the p-value of correlations. |
| correlogram | Correlogram. |
| create_trainer | Create a YamatClassifierTrainer object. |
| cross_validate_model5 | Cross-validate model 5 |
| density_plot_row_sd | Plot variablity of methylation signals across loci. |
| diagnose_tsne.coord | Diagnose multiple tSNE runs with coordinates plot. |
| diagnose_tsne.cor | Diagnose multiple tSNE runs with the correlations of... |
| explore_batch_effect | Explore batch effect. |
| explore_batch_effect_beta_value | Explore batch effect beta_value |
| explore_batch_effect_beta_value_pca_compute | Perform PCA on beta_value |
| explore_batch_effect_beta_value_rle | Explore batch effect beta_value - RLE. |
| explore_batch_effect_meth | Explore batch effect meth |
| explore_batch_effect_meth_pca_compute | Perform PCA on meth |
| explore_batch_effect_meth_rle | Explore batch effect meth - RLE. |
| explore_batch_effect_unmeth | Explore batch effect unmeth |
| explore_batch_effect_unmeth_pca_compute | Perform PCA on unmeth |
| explore_batch_effect_unmeth_rle | Explore batch effect unmeth - RLE. |
| find_pc_number.capper | Find PC number: Capper's method. |
| find_pc_number.var_frac | Find PC number: fraction of variance. |
| find_pc_number.yamat | Find PC number: yamat method. |
| get_and_filter_probes | Get and filter probes. |
| get_batch_effect_explore_dir | Get the directory of batch effect exploratory analysis. |
| get_batch_matrix | Get the batch matrix for fitting batch effect correction. |
| get_beta_value | Get beta value. |
| get_beta_value_adjusted | Get adjusted beta value. |
| get_beta_value_adjusted_rda | Get adjusted beta value Rda file path. |
| get_main_pca_plot | Main PCA plot |
| get_meth | Get meth. |
| get_meth_from_preprocessed_files | Get meth from preprocessed files. |
| get_preprocessed_dir | Get preprocessed file directory. |
| get_probes | Update probes of interest. |
| get_probes_from_scratch | Get probes of interest |
| get_probes_rda | Get probe ID file directory. |
| get_targets | Get targets. |
| get_trainer_rda | Get YamatClassifierTrainer Rda file. |
| get_unmeth | Get unmeth. |
| get_unmeth_from_preprocessed_files | Get unmeth from preprocessed files. |
| get_x_density_plot | PC x density plot |
| get_y_density_plot | PC y density plot |
| most_variable | Most variably methylated loci. |
| multiplot_tsne | Plot multiple tSNE results. |
| pca | PCA |
| pca123 | PCA step 1, 2, 3. |
| plot_pca_result | Plot PCA. |
| plot_relative_log_expression | Plot relative log expression. |
| plot_tsne | Plot tSNE result. |
| prepare_plot_data | Prepare PCA plot data |
| preprocess_dkfz | Preprocess DKFZ approach. |
| project_pc | Project to new basis. |
| run_fitsne | Computing t-SNE with fit-SNE algorithm. |
| run_rtsne | Computing t-SNE with 'Rtsne'. |
| select_features_boruta | Perform Boruta feature selection. |
| select_features_boruta2 | Perform Boruta feature selection with Boruta result. |
| select_features_ranger | Perform random forest feature selection with ranger package. |
| shuffle_matrix | Shuffle matrix. |
| train_batch_effect_model | Train the model for batch effect removal. |
| train_calibration_model_ridge | Train calibration model with ridge regularization. |
| train_model1 | Train model 1 |
| train_model1_inner_fold | Train model 1 - process the inner fold |
| train_model1_outer_fold | Train model 1 - Process the outer fold |
| train_model2 | Train model 2 |
| train_model2_inner_fold | Train model 2 - process the inner fold |
| train_model2_outer_fold | Train model 2 - Process the outer fold |
| train_model3 | Train model 3 |
| train_model3_inner_fold | Train model 3 - process the inner fold |
| train_model3_outer_fold | Train model 3 - Process the outer fold |
| train_model4 | Train model 4 |
| train_model4_inner_fold | Train model 4 - process the inner fold |
| train_model4_outer_fold | Train model 4 - Process the outer fold |
| train_model5_inner_fold | Train model 5 - process the inner fold |
| train_model5_outer_fold | Train model 5 - Process the outer fold |
| train_preprocess_pipe | Train preprocess pipeline |
| tsne | Run tSNE in batch mode. |
