run_benchmark {orthogene}R 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_mapped,
  benchmark_homologene = TRUE,
  benchmark_gprofiler = TRUE,
  run_convert_orthologs = TRUE,
  remove_failed_times = FALSE,
  save_path = tempfile(fileext = ".csv"),
  mc.cores = 1,
  verbose = TRUE
)

Arguments

species_mapped

Species names.

benchmark_homologene

Benchmark method "homologene".

benchmark_gprofiler

Benchmark method "gprofiler".

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


[Package orthogene version 1.0.2 Index]