R/check_species_babelgene.R

In neurogenomics/orthogene: Interspecies gene mapping

check_species_babelgene <- function(source_id,
                                    target_id) {
    all_species <- babelgene::species()
    if (is_human(target_id)) {
        if (!source_id %in% c(all_species$scientific_name, "Homo sapiens")) {
            stop_msg <- paste0(
                source_id, 
                " not in available input_species",
                " when method='babelgene'.\n",
                "Try method= 'gprofiler' or 'homologene' instead."
            )
            stop(stop_msg)
        }
    }
    if (is_human(source_id)) {
        if (!target_id %in% c(all_species$scientific_name, "Homo sapiens")) {
            stop_msg <- paste0(
                source_id, 
                " not in available output_species",
                " when method='babelgene'.\n",
                "Try method= 'gprofiler' or 'homologene' instead."
            )
            stop(stop_msg)
        }
    }
    if (all(!is_human(source_id), !is_human(target_id))) {
        stop_msg <- paste0(
            "Either input_species or output_species must be",
            " 'human' when method='babelgene'.\n",
            "Try method= 'gprofiler' or 'homologene' instead."
        )
        stop(stop_msg)
    }
}