Man pages for ethanmoyer/ICCE
Iterative Construction of Cyto-epigenetic Evolution
| add_data | Set data on either probe-node matrix at a new or existing... |
| betas_to_consensus_vector | Convert betas matrix to consensus vectors of probes for each... |
| build_icceTree | Fully generate probe-node matrix with available data |
| create_consensus_vector | Create consensus vector of probes for each group |
| create_node_matrix | Create node matrix used for tree walking functions |
| cut_tree | Recursively walk through a tree and structure remove... |
| fit_betas_to_distribution | Categorize betas based on bimodal distribution |
| fit_betas_to_distribution_p | Categorize betas based on bimodal distribution and return the... |
| generate_bimodal_distribution | Generate bimodal distribution on cell types |
| generate_branch_changes | Generate list of relevant probes for gain, loss, and change... |
| generate_p_values | Work on this... |
| get_leaves | Get the leaves of a tree |
| get_probes_of_gene | Get probes along a given gene |
| get_reference | Return reference data frame |
| get_relevant_genes | Find relevant genes for gain and loss of methylation |
| get_root | Get root of a tree |
| grow_off_leaf | Grow a tree at a given leaf node |
| icce_tree | Create icce tree object |
| inherit_parental_state | Inherit parental states to ambiguous nodes |
| initialize_probe_node_matrix | Initialize the probe-node matrix |
| ninternal_nodes | Get number of internal nodes on a tree |
| nleaves | Get number of leaves of a tree |
| nnodes | Get total number of nodes on a tree |
| nprobes | Get number of probes in consensus vector |
| read_IDAT | Load betas data |
| reconstruct_internal_nodes | Reconstruct internal nodes |
| relabel_node_matrix | Relabel node in probe-node matrix |
| relabel_tree | Relabel node on tree |
| remove_branches_from_node | Cut tree at specified node |
| remove_cell_types | Removes specific cell types from betas matrix |
| remove_intermediate_probes | Removes intermediate probes |
| remove_NA_probes | Removes NA probes |
| remove_sex_chr | Removes probes on sex chromosomes |
| remove_unapplicable_probes | Removes all inapplicable probes |
| remove_zero_parsimony_probes | Removes zero parsimony probes |
| save_data | Saves specified data with variable name to working directory |
| show_gene_track | Track the single probe resolution change of a gene |
| show_heatmap | Display heatmap of probes In progress |
| show_tree | Display tree |
| track_gene | Get proportion of probes methylated, unmethylated, ambiguous... |
| upgma_tree | Get UPGMA tree construction |
