diff --git a/R/data_processing.R b/R/data_processing.R index 17b7682..6611347 100644 --- a/R/data_processing.R +++ b/R/data_processing.R @@ -1325,6 +1325,10 @@ cleanMetaData <- function(duckdb_path, path, ref_file_path = "data_raw/") { dplyr::select("raw_entry", "clean_name", "short_name") |> dplyr::distinct() + # Define lab methods + lab_methods <- c("Disk diffusion", "MIC", "Broth dilution", "Agar dilution", "Biofosun Gram-positive panels broth dilution", + "Vitek_2-P607_card", "cation-adjusted Mueller-Hinton broth", "gradient_diffusion", "kirby-bauer_disc_diffusion") + dplyr::tbl(con, "filtered") |> tibble::as_tibble() |> dplyr::select("genome.genome_id") |> @@ -1332,12 +1336,17 @@ cleanMetaData <- function(duckdb_path, path, ref_file_path = "data_raw/") { tibble::as_tibble(), by = dplyr::join_by("genome.genome_id" == "genome_drug.genome_id")) |> dplyr::select( "genome.genome_id", "genome_drug.antibiotic", - "genome_drug.genome_name", "genome_drug.laboratory_typing_method", + "genome_drug.genome_name", "genome_drug.evidence", "genome_drug.laboratory_typing_method", "genome_drug.resistant_phenotype", "genome_drug.taxon_id", "genome_drug.pmid", "genome.collection_year", "genome.isolation_country", "genome.host_common_name", "genome.isolation_source", "genome.species" ) |> + dplyr::mutate(genome_drug.evidence = dplyr::case_when( + genome_drug.laboratory_typing_method %in% lab_methods ~ "Laboratory Method", + genome_drug.laboratory_typing_method == "Computational Prediction" ~ "Computational Method", + TRUE ~ genome_drug.evidence)) |> + dplyr::filter(genome_drug.evidence == "Laboratory Method") |> dplyr::left_join(clean_drug, by = c("genome_drug.antibiotic" = "original_drug")) |> dplyr::filter(!is.na(cleaned_drug)) |> dplyr::left_join(drug_class, by = c("cleaned_drug" = "drug")) |>