collapse_species: Collapse species pangenomes

In SWittouck/tidygenomes: A Grammar of Genome Data Manipulation

Collapse species pangenomes

Description

This function collapses each species to a single genome, and each orthogroup within a species to a single gene.

Usage

collapse_species(tg, core_threshold = 0.9)

Arguments

tg	A tidygenomes object
core_threshold	The minimum percentage of genomes within a species where a gene needs to be present to be considered a core gene

Details

A variable "species" must be present in the genome table for this function to work.

A variable "status" will be added to the gene table, indicating for each gene whether the orthogroup that gene belongs to is core or accessory within the species.

Value

A tidygenomes object

SWittouck/tidygenomes documentation built on Feb. 1, 2023, 9:50 p.m.