Man pages for ccfindR
Cancer Clone Finder
| assignCelltype | Cell type assignment via GSEA |
| basis | Basis matrices in an Object |
| basis-scNMFSet-method | Basis matrix accessor |
| basis-set | Generics for basis matrix assignment |
| basis-set-scNMFSet-method | Modify basis matrices |
| build_tree | Build tree connecting clusters at different ranks |
| ccfindR | ccfindR: Cancer Clone FindeR |
| cell_map | Plot heatmap of clustering coefficient matrix |
| cluster_id | Assign cells into clusters |
| coeff | Coefficient matrices in an Object |
| coeff-scNMFSet-method | Coefficient matrix accessor |
| coeff-set | Generics for coefficient matrix assignment |
| coeff-set-scNMFSet-method | Modify coefficient matrices |
| colData-scNMFSet-method | Sample annotation accessor |
| colData-set-scNMFSet-ANY-method | Cell annotation assignment |
| counts-scNMFSet-method | Accessor for count matrix |
| counts-set-scNMFSet-method | Assignment of count matrix |
| dbasis | Basis SD matrix accessor |
| dbasis-scNMFSet-method | Basis SD matrix accessor |
| dbasis-set | Basis SD matrix assignment |
| dbasis-set-scNMFSet-method | Modify dbasis matrices |
| dcoeff | Coeff SD matrix accessor |
| dcoeff-scNMFSet-method | Coeffcient SD matrix accessor |
| dcoeff-set | Coeff SD matrix assignment |
| dcoeff-set-scNMFSet-method | Modify dcoeff matrices |
| factorize | Maximum likelihood factorization |
| feature_map | Plot heatmap of basis matrix |
| filter_cells | Filter cells with quality control criteria |
| filter_genes | Filter genes with quality control criteria |
| gene_map | Plot heatmap of metagene matrix |
| measure | Factorization measures in an Object |
| measure-scNMFSet-method | Rank measure accessor |
| measure-set | Generics for factorization measure assignment |
| measure-set-scNMFSet-method | Modify factorization measure |
| meta_gene.cv | Meta gene table with CV |
| meta_genes | Find metagenes from basis matrix |
| newick | Generate Newick format tree string from tree list object |
| normalize_count | Normalize count data |
| optimal_rank | Determine optimal rank |
| plot_genes | Plot gene variance distributions |
| plot_tree | Plot cluster tree |
| ranks | Rank values in an Object |
| ranks-scNMFSet-method | Rank accessor |
| ranks-set | Generics for ranks assignment |
| ranks-set-scNMFSet-method | Modify ranks |
| read_10x | Read 10x data and generate scNMF object |
| remove_zeros | Remove rows or columns that are empty from an object |
| rename_tips | Rename tips of trees with cell types |
| rowData-scNMFSet-method | Feature annotation accessor |
| rowData-set-scNMFSet-method | Gene annotation assignment |
| scNMFSet | Create 'scNMFSet' object |
| scNMFSet-class | Class 'scNMFSet' for storing input data and results |
| show-scNMFSet-method | Display object |
| simulate_data | Generate simulated data for factorization |
| simulate_whx | Simulate factor matrices and data using priors |
| subset-methods | Subsetting scNMFSet object |
| vb_factorize | Bayesian NMF inference of count matrix |
| visualize_clusters | Visualize clusters |
| write_10x | Write 10x data files |
| write_meta | Write meta genes to a file |
