run_benchmark: Run benchmark tests

In neurogenomics/orthogene: Interspecies gene mapping

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.
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.
benchmark_homologene	Benchmark method "homologene".
benchmark_gprofiler	Benchmark method "gprofiler".
benchmark_babelgene	Benchmark method "babelgene".

Value

data.table with benchmark results

neurogenomics/orthogene documentation built on Jan. 30, 2024, 4:44 a.m.