Man pages for DCLEAR
Distance Based Cell Lineage Reconstruction
| add_deletion | add_deletion |
| add_dropout | add_dropout |
| as_igraph | Generic function for as_igraph |
| as_igraph-data.frame-method | as_igraph |
| as_igraph-phylo-method | as_igraph |
| as_lineage_tree | Generic function for as_lineage_tree |
| as_lineage_tree-phyDat-phylo-lineage_tree_config-method | as_lineage_tree |
| as_phylo | Generic function for as_phylo |
| as_phylo-igraph-method | as_phylo |
| DCLEAR | DCLEAR: A package for DCLEAR: Distance based Cell LinEAge... |
| dist_kmer_replacement_inference | Core function of computing kmer replacement distance |
| dist_replacement | Generic function for dist_replacement |
| dist_replacement-phyDat-kmer_summary-integer-method | Compute the kmer replacement distance |
| dist_replacement-phyDat-missing-integer-method | Compute the kmer replacement distance |
| dist_weighted_hamming | Generic function for dist_weighted_hamming |
| dist_weighted_hamming-phyDat-numeric-method | dist_weighted_hamming |
| downsample | Generic function for downsample |
| downsample-igraph-method | downsample |
| downsample-lineage_tree-method | downsample |
| get_distance_prior | get_distance_prior |
| get_leaves | Generic function for get_leaves |
| get_leaves-lineage_tree-method | get_leaves |
| get_node_names | get_node_names |
| get_replacement_probability | get_replacement_probability |
| get_sequence | get_sequence |
| get_transition_probability | get_transition_probability |
| lineages | Lineage data |
| positional_mutation_prob | positional_mutation_prob |
| process_sequence | Generic function for process_sequence |
| process_sequence-phyDat-method | Process sequences |
| prune | Generic function for prune |
| prune-igraph-method | prune |
| prune-lineage_tree-method | prune |
| random_tree | random_tree |
| rbind-phyDat-method | rbind |
| sample_mutation_outcome | sample_mutation_outcome |
| sample_mutation_site | sample_mutation_site |
| sample_outcome_prob | sample_outcome_prob |
| score_simulation | score_simulation |
| sim_seqdata | sim_seqdata |
| simulate | Generic function for simulate |
| simulate_core | simulate_core |
| simulate-lineage_tree_config-missing-method | simulate |
| simulate-lineage_tree_config-phyDat-method | simulate |
| substr_kmer | Generic function for substr_kmer |
| substr_kmer-kmer_summary-method | Subseting a kmer_summary object |
| subtract | Generic function for subtract |
| subtract-lineage_tree-lineage_tree-method | subtract |
| subtree | Generic function for subtree |
| subtree-lineage_tree-method | subtree |
| subtree-phylo-method | subtree |
| summarize_kmer | Generic function for summarize_kmer |
| summarize_kmer_core | summarize_kmer_core |
| summarize_kmer-phyDat-method | summarize_kmer |
| WH | WH |
| WH_train | Train weights for WH |
| WH_train_fit | Train weights for WH, and output distance object |
