RFGeneRank: Cross-validated Stable Predictive Gene Ranking for
Transcriptomics
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Documentation for package ‘RFGeneRank’ version 0.99.4
Help Pages
| align_datasets | Align and merge expression + metadata (genes by intersection; strict sample match) |
| apply_calibration | Apply stored calibration to a numeric vector of probabilities |
| calibrate_oof | Calibrate out-of-fold probabilities (isotonic or Platt) |
| calibration | Accessors for GeneRankFit |
| calibration-method | Accessors for GeneRankFit |
| calibration<- | Accessors for GeneRankFit |
| calibration<--method | Accessors for GeneRankFit |
| factor_dependence | Covariate dependence of gene contributions (SHAP/proxy; "expr" assay) |
| GeneRankFit-accessors | Accessors for GeneRankFit |
| id_map | Map gene identifiers using AnnotationDbi |
| imp | Accessors for GeneRankFit |
| imp-method | Accessors for GeneRankFit |
| imp<- | Accessors for GeneRankFit |
| imp<--method | Accessors for GeneRankFit |
| oof | Accessors for GeneRankFit |
| oof-method | Accessors for GeneRankFit |
| params | Accessors for GeneRankFit |
| params-method | Accessors for GeneRankFit |
| plot_confusion_heatmap | Confusion-matrix heatmap |
| plot_embed | Decision-space embedding (OOF probability space): PCA or UMAP |
| plot_embed_expr | Expression-space embedding (PCA or UMAP) of top RF genes |
| plot_importance | Feature importance (top genes) |
| plot_roc | ROC curve from OOF probabilities (single model) |
| plot_roc_multi | Multi-model ROC (guardrailed OOF) |
| plot_shap_dependence | SHAP dependence scatter for one gene (cached-first, robust, fast) |
| plot_sign_importance | Signed feature importance (directional effect) |
| prepare_data | Prepare matrices + metadata: align, (log) transform, batch correct, prefilter |
| rank_genes | Rank genes with batch-aware cross-validation (UMAP-free) |
| rfgr_crossval | Batch-aware cross-validation with optional ComBat modes (incl. frozen ComBat) |
| rfgr_plot_suite | One-call plot suite (optional file export) |
| shap_train_ranger | Compute a SHAP matrix using a single ranger model |
| sign_importance | Signed feature importance for RFGeneRank models |
| top_genes | Extract top predictive genes from a GeneRankFit |
| validate_genes | Validate a ranked gene set with alternate learners via k-fold CV |