run_benchmark: Run benchmark tests

View source: R/run_benchmark.R

run_benchmarkR Documentation

Run benchmark tests

Description

Runs benchmarks tests on all_genes and convert_orthologs across multiple species, using multiple methods ("homologene", and "gprofiler").

Usage

run_benchmark(
  species,
  method_list = c("homologene", "gprofiler", "babelgene"),
  run_convert_orthologs = TRUE,
  remove_failed_times = FALSE,
  save_path = tempfile(fileext = ".csv"),
  mc.cores = 1,
  verbose = TRUE
)

Arguments

species

Species names.

method_list

A list of ortholog conversion methods to benchmark.

run_convert_orthologs

Benchmark convert_orthologs function.

remove_failed_times

In instances where no genes were returned, set time to NA.

save_path

Path to save results to.

mc.cores

Number of cores to parallelise species across.

verbose

Print messages.

Value

data.table with benchmark results


neurogenomics/orthogene documentation built on April 17, 2025, 9:30 p.m.