Man pages for redsnic/CIMICE
CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
| annotate_mutational_matrix | Add samples and genes names to a mutational matrix |
| binary_radix_sort | Radix sort for a binary matrix |
| build_subset_graph | Remove transitive edges and prepare graph |
| build_topology_subset | Compute subset relation as edge list |
| chunk_reader | Gradually read a file from disk |
| CIMICE | CIMICE Package |
| compact_dataset | Compact dataset rows |
| computeDWNW | Down weights computation |
| computeDWNW_aux | Down weights computation (aux) |
| computeUPW | Up weights computation |
| computeUPW_aux | Up weights computation (aux) |
| compute_weights_default | Compute default weights |
| corrplot_from_mutational_matrix | Correlation plot from mutational matrix |
| corrplot_genes | Gene based correlation plot |
| corrplot_samples | Sample based correlation plot |
| dataset_preprocessing | Run CIMICE preprocessing |
| dataset_preprocessing_population | Run CIMICE preprocessing for poulation format dataset |
| draw_ggraph | ggplot graph output |
| draw_networkD3 | NetworkD3 graph output |
| draw_visNetwork | VisNetwork graph output (default) |
| example_dataset | Creates a simple example dataset |
| example_dataset_withFreqs | Creates a simple example dataset with frequency column |
| finalize_generator | Finalize generator normalizing edge weights |
| fix_clonal_genotype | Manage Clonal genotype in data |
| format_labels | Format labels for output object |
| gene_mutations_hist | Histogram of genes' frequencies |
| get_no_of_children | Get number of children |
| graph_non_transitive_subset_topology | Default preparation of graph topology |
| make_dataset | Dataset line by line construction: initialization |
| make_generator_stub | Create a stub for a generator |
| make_labels | Helper function to create labels |
| normalizeDWNW | Down weights normalization |
| normalizeUPW | Up weights normalization |
| perturb_dataset | Perturbate a boolean matrix |
| plot_generator | Plot a generator |
| prepare_generator_edge_set_command | Prepare a command to add edge weights to a generator |
| prepare_labels | Prepare node labels based on genotypes |
| quick_run | Run CIMICE defaults |
| read | Read a "CAPRI" file |
| read_CAPRI | Read a "CAPRI" file |
| read_CAPRIpop | Read a "CAPRIpop" file |
| read_CAPRIpop_string | Read "CAPRIpop" file from a string |
| read_CAPRI_string | Read "CAPRI" file from a string |
| read_MAF | Create mutational matrix from MAF file |
| read_matrix | Read dataset from an R matrix |
| remove_transitive_edges | Remove transitive edges from an edgelist |
| sample_mutations_hist | Histogram of samples' frequencies |
| select_genes_on_mutations | Filter dataset by genes' mutation count |
| select_samples_on_mutations | Filter dataset by samples' mutation count |
| set_generator_edges | Add edge weights to a generator |
| simulate_generator | Create datasets from generators |
| to_dot | Dot graph output |
| update_df | Dataset line by line construction: add a sample |
