medicc profiles files to foreground assessment — medicc_profiles_to

This function takes a medicc profile file (see dlptools::read_medicc_profiles()) and a tree, and marks if changes in states have occurred between parent nodes and tips.

Usage

medicc_profiles_to_foreground(
  medicc_profiles,
  phylogeny,
  cn_type = c("total", "allele")
)

Arguments

medicc_profiles: imported medicc profiles. See dlptools::read_medicc_profiles()
phylogeny: phylo object of phylogeny generated by medicc. See read_medicc_tree()
cn_type: string, 'total' or 'allele' to indicate which type of medicc output we are parsing. Characterization of changes is only done for total.

Value

table of tip data, their immediate parent states, and an inference of whether a foreground event has happened or not.