Adding genes(), traits(), updating search_gpmap()

Author: andrew-e

NAMESPACE

@@ -4,6 +4,7 @@ export(associations)
 export(associations_api)
 export(gene)
 export(gene_api)
+export(genes)
 export(genes_api)
 export(get_all_gene_pleiotropies)
 export(get_all_snp_pleiotropies)
@@ -22,6 +23,7 @@ export(search_variants_api)
 export(select_api)
 export(trait)
 export(trait_api)
+export(traits)
 export(traits_api)
 export(upload_gwas)
 export(variant)

R/genes.R

@@ -1,3 +1,29 @@
+#' @title Genes
+#' @description Get all genes from the API
+#' @return A dataframe containing all genes with the following columns:
+#'   \itemize{
+#'     \item id: the id of the gene
+#'     \item gene: the name of the gene
+#'     \item description: the description of the gene
+#'     \item gene_biotype: the gene biotype
+#'     \item chr: the chromosome of the gene
+#'     \item start: the start position of the gene
+#'     \item stop: the end position of the gene
+#'     \item strand: the strand of the gene
+#'     \item source: the source 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
+#'     \item num_study_extractions: the number of study extractions for this gene
+#'     \item num_coloc_groups: the number of coloc groups for this gene
+#'     \item num_coloc_studies: the number of studies that have coloc results for this gene
+#'     \item num_rare_groups: the number of rare groups for this gene
+#'   }
+#' @export
+genes <- function() {
+  genes <- genes_api()
+  return(genes$genes)
+}
+
 #' @title Gene
 #' @description A collection of studies that are associated with a particular gene.
 #' @param gene_id A numeric value specifying the gene id

R/pleiotropy.R

@@ -1,19 +1,29 @@
 #' @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
+#'   \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
+#'   }
 #' @export
 get_all_gene_pleiotropies <- function() {
   gene_pleiotropies <- gene_pleiotropies_api()
-  return(gene_pleiotropies)
+  return(gene_pleiotropies$genes)
 }
 
 #' @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
+#'   \itemize{
+#'     \item snp_id: the id of the SNP
+#'     \item display_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
+#'   }
 #' @export
 get_all_snp_pleiotropies <- function() {
   snp_pleiotropies <- snp_pleiotropies_api()
-  return(snp_pleiotropies)
+  return(snp_pleiotropies$snps)
 }

R/search.R

@@ -114,16 +114,8 @@ search_gpmap <- function(search_text) {
       TRUE ~ NA_character_
     )
 
-    search_results$info <- paste0(
-      ifelse(search_results$num_extractions > 0, paste0("Extractions: ", search_results$num_extractions, ", "), ""),
-      "Colocalisation Groups: ", search_results$num_coloc_groups, ", ",
-      "Colocalising Traits: ", search_results$num_coloc_studies, ", ",
-      "Rare Results: ", search_results$num_rare_results,
-      ifelse(search_results$type == "proxy_variant", paste0(", Rsquared: ", search_results$rsq), "")
-    )
-    search_results$rsq <- NULL
-
-    search_results <- dplyr::select(search_results, call, name, type, type_id, info)
+    columns_to_remove <- c("rsq", "name_lower", "alt_name", "alt_name_lower")
+    search_results <- dplyr::select(search_results, -dplyr::any_of(columns_to_remove))
   }
   return(search_results)
 }

R/traits.R

@@ -1,3 +1,29 @@
+#' @title Traits
+#' @description Get all traits from the API
+#' @return A dataframe containing all traits with the following columns:
+#'   \itemize{
+#'     \item id: the id of the trait
+#'     \item data_type: the data type of the trait
+#'     \item trait: the internal string id of the trait
+#'     \item trait_name: the name of the trait
+#'     \item trait_category: the trait category of the trait
+#'     \item variant_type: the type of variant
+#'     \item sample_size: the sample size of the trait
+#'     \item category: the category of the trait (continuous, categorical)
+#'     \item ancestry: the ancestry of the trait
+#'     \item heritability: the LDSC heritability score of the trait
+#'     \item heritability_se: the standard error of the LDSC heritability score of the trait
+#'     \item num_study_extractions: the number of study extractions for this trait
+#'     \item num_coloc_groups: the number of coloc groups for this trait
+#'     \item num_coloc_studies: the number of studies that have coloc results for this trait
+#'     \item num_rare_results: the number of rare results for this trait
+#'   }
+#' @export
+traits <- function() {
+  traits <- traits_api()
+  return(traits$traits)
+}
+
 #' @title Trait
 #' @description A collection of studies that are associated with a particular phenotype.
 #' A trait will include a common study and occasionally a rare study.
@@ -47,4 +73,5 @@ trait <- function(trait_id,
   if (include_associations) trait_info <- merge_associations(trait_info)
 
   return(trait_info)
-}
+}
+

man/genes.Rd

@@ -7,10 +7,15 @@ test_that("health() returns expected output", {
 })
 
 test_that("search_gpmap() returns expected output", {
-  result <- search_gpmap("hemoglobin")
+  result <- search_gpmap("haemoglobin")
   expect_type(result, "list")
+  print(result)
   expect_true(nrow(result) > 0)
-  expect_true(all(names(result) == c("call", "name", "type", "type_id", "info")))
+  expected_names <- c(
+    "call", "name", "type", "type_id", "num_coloc_groups",
+    "num_coloc_studies", "num_rare_results", "num_study_extractions"
+  )
+  expect_true(all(expected_names %in% names(result)))
 })
 
 test_that("trait() returns expected output", {
@@ -22,7 +27,7 @@ test_that("trait() returns expected output", {
 })
 
 test_that("variant() returns expected output", {
-  variant_id <- 5553693 
+  variant_id <- 5553693
   result <- variant(variant_id)
   expect_type(result, "list")
   expect_true(result$variant$id == variant_id)
@@ -48,12 +53,24 @@ test_that("associations() returns expected output", {
 
 test_that("get_all_gene_pleiotropies() returns expected output", {
   result <- get_all_gene_pleiotropies()
-  expect_type(result$genes, "list")
-  expect_true(nrow(result$genes) > 0)
+  expect_type(result, "list")
+  expect_true(nrow(result) > 0)
 })
 
 test_that("get_all_snp_pleiotropies() returns expected output", {
   result <- get_all_snp_pleiotropies()
-  expect_type(result$snps, "list")
-  expect_true(nrow(result$snps) > 0)
+  expect_type(result, "list")
+  expect_true(nrow(result) > 0)
+})
+
+test_that("genes() returns expected output", {
+  result <- genes()
+  expect_type(result, "list")
+  expect_true(nrow(result) > 0)
+})
+
+test_that("traits() returns expected output", {
+  result <- traits()
+  expect_type(result, "list")
+  expect_true(nrow(result) > 0)
 })