get_lineage: Build lineage from a given rc_index, using only P <= p_thresh

In reptalex/dendromap: dendromap: R package for using time-scaled reference trees to scale microbial phylogenies.

Description

Build lineage from a given rc_index, using only P <= p_thresh

Usage

get_lineage(
  basal_ix,
  p_thresh = 1,
  rc_relations,
  rc_table,
  row.tree,
  rowDescendants,
  colDescendants
)

Arguments

basal_ix	index found in rc_table$rc_index
p_thresh	Positive numeric, threshold P-value for inclusion of rc-pairs
rc_relations
rc_table	see make_rc_table
row.tree	phylo class object
rowDescendants	List of descendants made from edge_registry. Element i contains all edges descendant from edge i in the row tree
colDescendants	List of descendants made from edge_registry. Element j contains all edges descendant from edge j in the column tree

reptalex/dendromap documentation built on April 19, 2021, 5:13 a.m.