denominator: internal function

In Chien-Hsun/rePhylo: Re-investigating and Improving Phylogenies

Description

Internal function of rePhylo

Usage

denominator(
  x,
  ref,
  refinfo,
  split = NULL,
  c.out = FALSE,
  sub_coverage = NULL,
  max.tip = NULL,
  bp = NULL
)

Arguments

x	x
ref	ref
refinfo	refinfo
split	a character indicates the symbol used to separate species names and gene id for gene family trees. Defaults to NULL.
c.out	logical. Whether the closest outgroup species are required to exist. Defaults to FALSE.
sub_coverage	a numeric to specify the species coverage of the clades of each node. Used as percent when <= 1, and as count when > 1. Defaults to NULL.
max.tip	an integer specifying the max number of tips for the coverage filtering. Applied only when sub_coverage is set as percent (<= 1). Used as a cutoff for coverage as N tips as for deep nodes having large clades. Defaults to NULL.
bp	a numeric specify the minimum bp value for the node. Defaults to NULL.

See Also

concor.node detect_closest_out_for_GD filter_GD_by_coverage

Chien-Hsun/rePhylo documentation built on May 19, 2020, 3:15 a.m.