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Read and parse Orthofinder summary statistics

Source: R/file_import.R
read_orthofinder_stats.Rd

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)