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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,101 @@ | ||
| #' Map disease | ||
| #' | ||
| #' Map disease IDs (e.g. "OMIM:101200") to names (e.g. "Apert syndrome") | ||
| #' @inheritParams add_ | ||
| #' @param dat A data.table with a column of disease IDs. | ||
| #' @param id_col The name of the column with the disease IDs. | ||
| #' @param fields The fields to extract from the API response. | ||
| #' @param return_dat Return the data.table with the mapped fields. | ||
| #' @param use_api Use the API to get the disease names and descriptions. | ||
| #' Otherwise, use a cached data.table (\code{disease_map}). | ||
| #' @inheritParams KGExplorer::set_cores | ||
| #' @source \href{https://ontology.jax.org/api/network/docs}{HPO API docs} | ||
| #' @source \href{https://github.com/obophenotype/human-phenotype-ontology/issues/10232}{HPO GitHub Issue} | ||
| #' @export | ||
| #' @examples | ||
| #' dat <- HPOExplorer::load_phenotype_to_genes() | ||
| #' out <- map_disease(dat = dat, workers=1) | ||
| map_disease <- function(dat, | ||
| id_col="disease_id", | ||
| fields=c("disease","categories","genes")[1], | ||
| use_api=TRUE, | ||
| return_dat=FALSE, | ||
| workers=NULL, | ||
| all.x = TRUE, | ||
| allow.cartesian = FALSE | ||
| ){ | ||
| # res <- httr::GET( | ||
| # "https://ontology.jax.org/api/network/annotation/OMIM%3A101200", | ||
| # httr::add_headers(accept = "application/json") | ||
| # ) | ||
| # cont <- httr::content(res) | ||
|
|
||
| # Define the URL and headers | ||
| if(!id_col %in% names(dat)){ | ||
| stop("id_col not found in dat.") | ||
| } | ||
| if(!all(c("disease_name","disease_description") %in% names(dat))){ | ||
| messager("Adding disease_name and disease_description.") | ||
| #### Slow but up-to-date #### | ||
| if(use_api || length(fields)>1){ | ||
| map_disease_i <- function(id){ | ||
| url <- URLencode( | ||
| ## encode URL | ||
| paste0("https://ontology.jax.org/api/network/annotation/",id) | ||
| ) | ||
| ## get content | ||
| cont <- jsonlite::fromJSON(url) | ||
| ## Extract names | ||
| cont$disease <- data.table::as.data.table(cont$disease) | ||
| cont$disease|> data.table::setnames( | ||
| c("name","description","mondoId"), | ||
| c("disease_name","disease_description","mondo_id")) | ||
| cont$genes <- data.table::as.data.table(cont$genes) | ||
| cont$categories <- lapply(cont$categories, function(x){ | ||
| data.table::data.table(x) | ||
| })|> | ||
| data.table::rbindlist(idcol = "hpo_group", fill=TRUE) |> | ||
| data.table::setnames(c("id","name"),c("hpo_id","hpo_name")) | ||
| names(cont$categories) <- gsub("[.]","_",names(cont$categories)) | ||
|
|
||
| #### Return #### | ||
| if(length(fields)==1){ | ||
| return(cont[[fields]]) | ||
| } else { | ||
| return(cont) | ||
| } | ||
| } | ||
| #### Iterate #### | ||
| ids <- unique(dat[[id_col]]) | ||
| BPPARAM <- KGExplorer::set_cores(workers = workers) | ||
| res <- BiocParallel::bplapply(X = stats::setNames(ids,ids), | ||
| FUN = map_disease_i, | ||
| BPPARAM = BPPARAM) | ||
| if(length(fields)==1){ | ||
| res <- data.table::rbindlist(res, fill=TRUE) | ||
| if(return_dat){ | ||
| dat <- merge(dat, res, | ||
| by.x=id_col, | ||
| by.y = "id", | ||
| all.x = TRUE) | ||
| return(dat) | ||
| } | ||
| } | ||
| return(res) | ||
| #### Fast but potentially out-of-date #### | ||
| } else{ | ||
| disease_map <- KGExplorer::get_data_package(name = "disease_map", | ||
| package = "HPOExplorer") | ||
| dat <- data.table::merge.data.table( | ||
| dat, | ||
| disease_map, | ||
| by = "disease_id", | ||
| all.x = all.x, | ||
| allow.cartesian = allow.cartesian) | ||
| return(dat) | ||
| } | ||
| } else { | ||
| messager("disease_name and disease_description already in dat.") | ||
| return(dat) | ||
| } | ||
| } |
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