filterStats: filterStats

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

Description

Function for gather filtration statistics, used internally by filterSummary

Usage

filterStats(
  data = NULL,
  filter.name = c("alignment_length", "count_pis", "proportion_pis",
    "proportion_samples"),
  min.alignments = 5,
  filter.values = NULL,
  align.dataset = NULL
)

Arguments

data	alignment summmary data from alignmentSummary function
filter.name	Name of the filter being passed. Only one can be used at a time.
min.alignments	minimum number of alignments to keep a filtration scheme
filter.values	the filter values for the given scheme
align.dataset	select three colors to plot your pie.plot

Value

Alignment statistics for the specific filteration scheme provided

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.