filterConcordance: filterConcordance

In chutter/FilterZone: R Package For Detecting the Anomaly Zone and Alignment Filtering in Large Phylogenomic Datasets

Description

Function for obtaining filtered concordance factor data

Usage

filterConcordance(
  input.dir = NULL,
  clade.list = NULL,
  outgroups = NULL,
  all.data = TRUE
)

Arguments

input.dir	summary data file from filterSummary
clade.list	a named list of clades of interest to test for concordance factors
outgroups	outgroups to root the tree
all.data	select T to obtain all the node data or F to obtain only nodes from clade list

Value

data.frame with concordance factor data for each filtered replicate

Examples

your.tree = ape::read.tree(file = "file-path-to-tree.tre")
astral.data = astralPlane(astral.tree = your.tree,
                          outgroups = c("species_one", "species_two"),
                          tip.length = 1)

chutter/FilterZone documentation built on Dec. 19, 2021, 4:07 p.m.