Man pages for ethanmoyer/MethylConstruct
| add_data | Add to probe-node matrix at a new node |
| betas_to_consensus_vector | Converts betas matrix to consensus vectors of probes for each... |
| create_consensus_vector | Create consensus vector of probes for each group VALIDATED |
| create_node_matrix | Node matrix used for tree walking VALIDATED |
| cut_tree | Recursively walk through tree and remove descendants. |
| fit_betas_to_distribution | Categorize betas based on bimodal distribution VALIDATED |
| generate_bimodal_distribution | Generate bimodal distribution VALIDATED |
| generate_branch_changes | Relevant probes for gain, loss, and change in methylation... |
| generate_probe_node_matrix | Fully generate probe-node matrix with available data... |
| get_leaves | Leaves of a tree |
| get_probes_of_gene | Probes along a given gene VALIDATED |
| get_reference | Returns reference file VALIDATED |
| get_relevant_genes | Relevant genes for gain and loss of methylation VALIDATED |
| get_root | Root of a tree VALIDATED |
| grow_off_leaf | Grow a tree at a given leaf node |
| inherit_parental_state | Inherit parental states to ambiguous nodes VALIDATED |
| initialize_probe_node_matrix | Initialize the probe-node matrix VALIDATED |
| ninternal_nodes | Number of internal nodes on a tree VALIDATED |
| nleaves | Number of leaves of a tree |
| nnodes | Total number of nodes on a tree VALIDATED |
| nprobes | Number of probes in data VALIDATED |
| read_IDAT | Load beta data |
| reconstruct_internal_nodes | Reconstruct internal nodes VALIDATED |
| 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 | Remove specific cell types from betas matrix VALIDATED |
| remove_intermediate_probes | Removes intermediate probes VALIDATED |
| remove_NA_probes | Removes NA probes VALIDATED |
| remove_sex_chr | Remove probes on sex chromosomes VALIDATED |
| remove_unapplicable_probes | Removes all inapplicable probes VALIDATED |
| remove_zero_parsimony_probes | Removes zero parsimony probes VALIDATED |
| 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 | Relabel node in probe-node matrix |
| show_tree | Display tree VALIDATED |
| track_gene | Proportion of probes methylated, unmethylated, ambiguous at... |
| upgma_tree | UPGMA tree construction VALIDATED |
