filterAnomalies: filterAnomalies

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

Description

Applies the anomaly zone calculation across all filtered datasets and combines with filter summary data for downstream analyses

Usage

filterAnomalies(astral.directory = NULL, outgroups = NULL, filter.data = NULL)

Arguments

astral.directory	directory of filtered astral results
outgroups	outgroups to root your tree
filter.data	your master filtered dataset summary stats

Value

a data.table of anomaly zone data calculated for all nodes in your tree

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.