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]