replace_ariba_cluster_names — replace_ariba_cluster

rename amr headers, converting ariba cluster to common prefix

replace_ariba_cluster_names(annotated_amr_data, max_number_genes = 3)

Arguments

annotated_amr_data	acquired_amr_data obtained using the ghruR::get_data_for_country(country_value = "<COUNTRY>", type_value = "AMR <SPECIES>", AMR_type = "acquired") and annotated using the annotate_amr_data function
max_number_genes	The maximum number of genes names in a column label before a common prefix is taken

final_long_amr_data A long format ready for filtering with columns amr_gene_column, refseq_nucleotide_accession, assembled, pct_id, ctg_cov