Adding new pleiotropy data access functions (#11)

Author: andrew-e

NAMESPACE

@@ -5,6 +5,8 @@ export(associations_api)
 export(gene)
 export(gene_api)
 export(genes_api)
+export(get_all_gene_pleiotropies)
+export(get_all_snp_pleiotropies)
 export(health_api)
 export(ld_matrix)
 export(ld_matrix_by_snp_id_api)

R/api.r

@@ -357,4 +357,27 @@ associations_api <- function(snp_ids, study_ids) {
   associations <- httr::content(associations, "text", encoding = "UTF-8")
   associations <- jsonlite::fromJSON(associations)
   return(associations)
+}
+
+
+#' @title Get All Gene Pleiotropies API
+#' @description Get all gene pleiotropies from the API
+#' @return A list containing the gene pleiotropies
+gene_pleiotropies_api <- function() {
+  url <- paste0(getOption("gpmap_url"), "/v1/pleiotropy/genes")
+  gene_pleiotropies <- httr::GET(url, httr::timeout(timeout_seconds))
+  gene_pleiotropies <- httr::content(gene_pleiotropies, "text", encoding = "UTF-8")
+  gene_pleiotropies <- jsonlite::fromJSON(gene_pleiotropies)
+  return(gene_pleiotropies)
+}
+
+#' @title Get All SNP Pleiotropies API
+#' @description Get all SNP pleiotropies from the API
+#' @return A list containing the SNP pleiotropies
+snp_pleiotropies_api <- function() {
+  url <- paste0(getOption("gpmap_url"), "/v1/pleiotropy/snps")
+  snp_pleiotropies <- httr::GET(url, httr::timeout(timeout_seconds))
+  snp_pleiotropies <- httr::content(snp_pleiotropies, "text", encoding = "UTF-8")
+  snp_pleiotropies <- jsonlite::fromJSON(snp_pleiotropies)
+  return(snp_pleiotropies)
 }

R/pleiotropy.R

@@ -0,0 +1,19 @@
+#' @title Get All Gene Pleiotropies
+#' @description Get gene pleiotropy from the API by gene id
+#' @return A list containing the gene pleiotropy
+#' @inheritSection gene_pleiotropy_doc gene_pleiotropy_dataframe
+#' @export
+get_all_gene_pleiotropies <- function() {
+  gene_pleiotropies <- gene_pleiotropies_api()
+  return(gene_pleiotropies)
+}
+
+#' @title Get All SNP Pleiotropies
+#' @description Get all SNP pleiotropies from the API
+#' @return A list containing the SNP pleiotropies
+#' @inheritSection snp_pleiotropy_doc snp_pleiotropy_dataframe
+#' @export
+get_all_snp_pleiotropies <- function() {
+  snp_pleiotropies <- snp_pleiotropies_api()
+  return(snp_pleiotropies)
+}

R/shared_docs.R

@@ -188,4 +188,32 @@ genes_in_region_doc <- function() {}
 #'   \item r: the r value between the lead and variant SNPs
 #' }
 #' @keywords internal
-ld_doc <- function() {}
+ld_doc <- function() {}
+
+#' @title Gene Pleiotropies Dataframe Documentation
+#' @description Shared documentation for gene_pleiotropies dataframe columns
+#' @section gene_pleiotropies_dataframe:
+#' The gene_pleiotropies dataframe contains information about which genes are pleiotropic.
+#' It has the following columns:
+#' \itemize{
+#'   \item gene_id: the id of the gene
+#'   \item gene: the name of the gene
+#'   \item : distinct_trait_categories the number of trait categories that the gene is associated with via coloc groups
+#'   \item : distinct_protein_coding_genes the number of genes that the gene is associated with via coloc groups
+#' }
+#' @keywords internal
+gene_pleiotropies_doc <- function() {}
+
+#' @title SNP Pleiotropies Dataframe Documentation
+#' @description Shared documentation for snp_pleiotropies dataframe columns
+#' @section snp_pleiotropies_dataframe:
+#' The snp_pleiotropies dataframe contains information about which SNPs are pleiotropic.
+#' It has the following columns:
+#' \itemize{
+#'   \item snp_id: the id of the SNP
+#'   \item snp: the name of the SNP
+#'   \item : distinct_trait_categories the number of trait categories that the SNP is associated with via coloc groups
+#'   \item : distinct_protein_coding_genes the number of genes that the SNP is associated with via coloc groups
+#' }
+#' @keywords internal
+snp_pleiotropies_doc <- function() {}