read_orthofinder_stats: Read and parse Orthofinder summary statistics

In almeidasilvaf/cogeqc: Systematic quality checks on comparative genomics analyses

Read and parse Orthofinder summary statistics

Description

Read and parse Orthofinder summary statistics

Usage

read_orthofinder_stats(stats_dir = NULL)

Arguments

stats_dir

Path to directory containing Orthofinder's comparative genomics statistics. In your Orthofinder results directory, this directory is named Comparative_Genomics_Statistics.

Value

A list of data frames with the following elements:

1. stats A data frame of summary stats per species with the following variables:

   Species

   Factor of species names.

   N_genes

   Numeric of number of genes.

   N_genes_in_OGs

   Numeric of number of genes in orthogroups.

   Perc_genes_in_OGs

   Numeric of percentage of genes in orthogroups.

   N_ssOGs

   Numeric of number of species-specific orthogroups.

   N_genes_in_ssOGs

   Numeric of number of genes in species-specific orthogroups.

   Perc_genes_in_ssOGs

   Numeric of percentage of genes in species-specific orthogroups.

   Dups

   Integer with number of duplications per species.

2. og_overlap A symmetric data frame of pairwise orthogroup overlap between species.

3. duplications A 2-column data frame with node IDs in the first column and number of gene duplications (50% support) in the second column.

Examples

stats_dir <- system.file("extdata", package = "cogeqc")
ortho_stats <- read_orthofinder_stats(stats_dir)

almeidasilvaf/cogeqc documentation built on Jan. 29, 2024, 7:20 a.m.