generate_branch_changes: Generate list of relevant probes for gain, loss, and change...
In ethanmoyer/ICCE: Iterative Construction of Cyto-epigenetic Evolution

Description Usage Arguments Value Examples

This function returns relevant probe lists for each node that exhibits either a gain or a loss in methylation status. It also returns three sets of branch labels: number of methylation changes, number of methylation gains, and number of methylation losses. These labels can be given to the show_tree function as an edge labels parameter to visualize this data.

1	generate_branch_changes(icceTree)

`icceTree`	icceTree data structure
`probe_node_matrix`	probe-node matrix storing the methylation status across all probes and nodes on a tree

a structure containing a list of probes with differentially methylated probes for each node (gain and loss stored separately), a list of branch labels for the number of total changes in methylation, a list of branch labels for the number of gains in methylation, and a list of branch labels for the number of losses in methylation

probe_information <- generate_branch_changes(icceTree)
relevant_probes <- probe_information$relevant_probes
total_changes_label <- probe_information$total_changes_label
meth_gains_label <- probe_information$meth_gains_label
meth_losses_label <- probe_information$meth_losses_label