get_annotated_point_amr_data

convert amr dataframe to long format and join to NCBI metadata

get_annotated_point_amr_data(point_amr_data, species, annotation_type)

Arguments

species	one of campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, klebsiella, mycobacterium_tuberculosis, neisseria_gonorrhoeae, salmonella
annotation_type	Either mutations (all mutations in genes that have fully assembled), incomplete (all genes that are not fully assembled)
amr_data	point amr data obtained using the ghruR::get_data_for_country(country_value = "<COUNTRY>", type_value = "AMR <SPECIES>", AMR_type = "point")

Value

annonated_amr_data dataframe with amr data converted to long format and annotated with NCBI metadata