get_target_genes: Lists genes without missingness Takes a list of genes and...

In svteichman/TreeVizPackage: Tree Visualization Package

Lists genes without missingness Takes a list of genes and returns the list with genes removed that are missing one or more tips.

Description

Lists genes without missingness Takes a list of genes and returns the list with genes removed that are missing one or more tips.

Usage

get_target_genes(
  gene_names,
  path = "",
  tail = ".fa",
  exclude_outgroup = FALSE,
  outgroup = NULL
)

Arguments

gene_names	A list of gene names that correspond with alignments to examine
path	The file path to the gene alignments, default is "
tail	The extension to the gene alignments, default is ".fa
exclude_outgroup	Binary variable, if true target genes will not need to be in the outgroup genome.
outgroup	Name of the outgroup, required if exclude_outgroup = T.

Value

A list containing a subset of the gene_names list only including names of genes without missingness and the full presence matrix.

svteichman/TreeVizPackage documentation built on June 22, 2022, 11:21 p.m.