filterSummary: filterSummary

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

Description

Summarizes filtered datasets when provided with filter parameters

Usage

filterSummary(
  alignment.data = NULL,
  alignment.folder = NULL,
  dataset.name = NULL,
  file.out = NULL,
  length.filters = c(0),
  sample.filters = c(0),
  prop.pis.filters = c(0),
  count.pis.filters = c(0)
)

Arguments

alignment.data	Alignment summary stats calculcated from summarizeAlignments
alignment.folder	The alignment folder from which the stats were calculated from in alignment.data
dataset.name	The name of your dataset, where all filtered datasets will be placed in this folder
file.out	if you wish to save to file, provide a file name for the summary
length.filters	Your selected length filters as a vector of values for the alignment length
sample.filters	Your selected sampling fraction filters as a vector of values between 0-1
prop.pis.filters	Your selected parsimony informatives sites filter as a vector of values between 0-1
count.pis.filters	Your selected parsimony informatives sites filter as a vector of base pair counts

Value

Returns a summary of your selected filters applied to the dataset

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.