Get number of shared orthogroups between species pairs — get_og_overlap • cogeqc

Get number of shared orthogroups between species pairs

Usage

get_og_overlap(orthogroups)

Arguments

orthogroups: A 3-column data frame with columns Orthogroup, Species, and Gene. This data frame can be created from the 'Orthogroups.tsv' file generated by OrthoFinder with the function read_orthogroups().

Value

A data frame with the following variables:

sp1: Character, name of species 1.
sp2: Character, name of species 2.
og_overlap: Numeric, number of shared orthogroups.

Examples

path <- system.file("extdata", "Orthogroups.tsv.gz", package = "cogeqc")
orthogroups <- read_orthogroups(path)
ov_df <- get_og_overlap(orthogroups)