read_pangenome: Read pangenome from a file or folder

In SWittouck/tidygenomes: A Grammar of Genome Data Manipulation

Read pangenome from a file or folder

Description

This function reads a file or folder containing a pangenome, as created by tools such as OrthoFinder, and returns a genes tibble with the genome and orthogroup of each gene.

Usage

read_pangenome(path)

Arguments

path	Path to a file or folder containing the pangenome

Details

The path can currently only be an OrthoFinder Orthogroups folder (for OrthoFinder >= v2.3.1), or Results folder (older versions). In the future, this can be extended to output folders or files from other pangenome tools.

Value

A tibble with the variables gene, genome and orthogroup

Examples

## Not run: 
genes <- read_pangenome("Results_Sep06")

## End(Not run)

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