complete dynamic association endpoints; also rename calculate_eqtls()…

… to calculate_splicing_quantitative_trait_loci()

.Rbuildignore

@@ -10,3 +10,5 @@
 ^README\.Rmd$
 ^codecov\.yml$
 ^.vscode$
+^doc$
+^Meta$

.gitignore

@@ -4,3 +4,5 @@ docs
 .vscode
 inst/doc
 .Renviron
+/doc/
+/Meta/

NAMESPACE

@@ -1,8 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
 export(available_tissueSiteDetailIds)
-export(calculate_eqtls)
+export(calculate_expression_quantitative_trait_loci)
 export(calculate_ieqtls)
+export(calculate_isqtls)
+export(calculate_splicing_quantitative_trait_loci)
 export(get_annotation)
 export(get_clustered_median_exon_expression)
 export(get_clustered_median_gene_expression)

R/calculate_expression_quantitative_trait_loci.R

@@ -0,0 +1,91 @@
+#' Calculate Expression Quantitative Trait Loci
+#'
+#' @description Calculate your own eQTLs
+#'
+#' - This service calculates the gene-variant association for any given pair of gene and variant, which may or may not be significant.
+#' - This requires as input a GENCODE ID, GTEx variant ID, and tissue site detail ID.
+#'
+#' By default, the calculation is based on the latest GTEx release.
+#'
+#' [GTEx Portal API documentation](https://gtexportal.org/api/v2/redoc#tag/Dynamic-Association-Endpoints/operation/calculate_expression_quantitative_trait_loci_api_v2_association_dyneqtl_get).
+#'
+#' @details Notes on output:
+#'
+#' * Beta and standard error are recorded in columns `nes` and `error` respectively (see [GTEx FAQs](https://gtexportal.org/home/faq#nes_beta))
+#' * `variantId` contains (in order) chromosome, position, reference allele, alternative allele and human genome build separated by underscores. The reference and alternative alleles for "chr1_13550_G_A_b38" for example are "G" and "A" respectively.
+#' * See examples for how to calculate minor and alternative allele frequencies.
+#'
+#' Notes on input:
+#'
+#' * Argument `variantId` also accepts RSIDs.
+#'
+#' @inheritParams gtexr_arguments
+#'
+#' @return A tibble.
+#' @export
+#' @family Dynamic Association Endpoints
+#'
+#' @examples
+#' \dontrun{
+#' # perform request - returns a tibble with a single row
+#' calculate_expression_quantitative_trait_loci(tissueSiteDetailId = "Whole_Blood",
+#'                                              gencodeId = "ENSG00000203782.5",
+#'                                              variantId = "rs79641866")
+#'
+#' # unnest list columns with tidyr::unnest()
+#' calculate_expression_quantitative_trait_loci(tissueSiteDetailId = "Whole_Blood",
+#'                                              gencodeId = "ENSG00000203782.5",
+#'                                              variantId = "rs79641866") |>
+#'   tidyr::unnest(c("data", "genotypes"))
+#'
+#' # to calculate minor and alternative allele frequencies
+#' calculate_expression_quantitative_trait_loci(
+#'   tissueSiteDetailId = "Liver",
+#'   gencodeId = "ENSG00000237973.1",
+#'   variantId = "rs12119111"
+#' ) |>
+#'  dplyr::bind_rows(.id = "rsid") |>
+#'
+#'  tidyr::separate(
+#'    col = "variantId",
+#'    into = c(
+#'      "chromosome",
+#'      "position",
+#'      "reference_allele",
+#'      "alternative_allele",
+#'      "genome_build"
+#'    ),
+#'    sep = "_"
+#'  ) |>
+#'
+#'  # ...then ascertain alternative_allele frequency
+#'  dplyr::mutate(
+#'    alt_allele_count = (2 * homoAltCount) + hetCount,
+#'    total_allele_count = 2 * (homoAltCount + hetCount +  homoRefCount),
+#'    alternative_allele_frequency = alt_allele_count / total_allele_count
+#'  ) |>
+#'
+#'  dplyr::select(
+#'    rsid,
+#'    beta = nes,
+#'    se = error,
+#'    pValue,
+#'    minor_allele_frequency = maf,
+#'    alternative_allele_frequency,
+#'    chromosome:genome_build,
+#'    tissueSiteDetailId
+#'  )
+#' }
+calculate_expression_quantitative_trait_loci <- function(tissueSiteDetailId,
+                           gencodeId,
+                           variantId,
+                           datasetId = "gtex_v8") {
+  result <- gtex_query("association/dyneqtl",
+             return_raw = TRUE)
+  result$data <- list(tibble::tibble(data = as.numeric(result$data)))
+  result$genotypes <- list(tibble::tibble(genotypes = as.integer(result$genotypes)))
+
+  result <- tibble::as_tibble(result)
+
+  return(result)
+}

R/calculate_ieqtls.R

@@ -1,10 +1,13 @@
 #' Calculate Ieqtls
 #'
-#'Calculate your own Cell Specific eQTLs.
+#' @description Calculate your own Cell Specific eQTLs.
 #'
-#'- This service calculates the gene-variant association for any given pair of gene and variant, which may or may not be significant.
-#'- This requires as input a GENCODE ID, GTEx variant ID, and tissue site detail ID.
-#'By default, the calculation is based on the latest GTEx release.
+#' - This service calculates the gene-variant association for any given pair of gene and variant, which may or may not be significant.
+#' - This requires as input a GENCODE ID, GTEx variant ID, and tissue site detail ID.
+#'
+#' By default, the calculation is based on the latest GTEx release.
+#'
+#' [GTEx Portal API documentation](https://gtexportal.org/api/v2/redoc#tag/Dynamic-Association-Endpoints/operation/calculate_ieqtls_api_v2_association_dynieqtl_get).
 #'
 #' @inheritParams gtexr_arguments
 #'
@@ -19,7 +22,7 @@
 #'                  tissueSiteDetailId = "Adipose_Subcutaneous",
 #'                  gencodeId = "ENSG00000203782.5",
 #'                  variantId = "chr1_1099341_T_C_b38")
-#'}
+#' }
 calculate_ieqtls <-
   function(cellType,
            tissueSiteDetailId,

R/calculate_isqtls.R

@@ -0,0 +1,41 @@
+#' Calculate Isqtls
+#'
+#' @description Calculate your own Cell Specific sQTLs.
+#'
+#' - This service calculates the gene-variant association for any given pair of gene and variant, which may or may not be significant.
+#' - This requires as input a GENCODE ID, GTEx variant ID, and tissue site detail ID.
+#'
+#' By default, the calculation is based on the latest GTEx release.
+#'
+#' [GTEx Portal API documentation](https://gtexportal.org/api/v2/redoc#tag/Dynamic-Association-Endpoints/operation/calculate_ieqtls_api_v2_association_dynieqtl_get).
+#'
+#' @inheritParams gtexr_arguments
+#'
+#' @return A tibble.
+#' @export
+#' @family Dynamic Association Endpoints
+#'
+#' @examples
+#' \dontrun{
+#' # perform request
+#' calculate_isqtls(cellType = "Neutrophils",
+#'                  tissueSiteDetailId = "Whole_Blood",
+#'                  phenotypeId = "chr1:15947:16607:clu_40980:ENSG00000227232.5",
+#'                  variantId = "chr1_1099341_T_C_b38")
+#' }
+calculate_isqtls <-
+  function(cellType,
+           tissueSiteDetailId,
+           phenotypeId,
+           variantId,
+           datasetId = "gtex_v8") {
+    gtex_query(endpoint = "association/dynisqtl", return_raw = TRUE) |>
+      purrr::imap(\(x, idx) ifelse(is.list(x),
+                                   tibble::tibble(
+                                     data = purrr::map_depth(x,
+                                                             purrr::pluck_depth(x) - 2,
+                                                             unlist)
+                                   ),
+                                   x)) |>
+      tibble::as_tibble()
+  }

R/calculate_splicing_quantitative_trait_loci.R

@@ -0,0 +1,31 @@
+#' Calculate Splicing Quantitative Trait Loci
+#'
+#' @description
+#' [GTEx Portal API documentation](https://gtexportal.org/api/v2/redoc#tag/Dynamic-Association-Endpoints/operation/calculate_splicing_quantitative_trait_loci_api_v2_association_dynsqtl_get).
+#'
+#' @inheritParams gtexr_arguments
+#'
+#' @return A tibble.
+#' @export
+#' @family Dynamic Association Endpoints
+#'
+#' @examples
+#' \dontrun{
+#' # perform request - returns a tibble with a single row
+#' calculate_splicing_quantitative_trait_loci(
+#'   tissueSiteDetailId = "Whole_Blood",
+#'   phenotypeId = "chr1:15947:16607:clu_40980:ENSG00000227232.5",
+#'   variantId = "chr1_14677_G_A_b38")
+#' }
+calculate_splicing_quantitative_trait_loci <- function(tissueSiteDetailId,
+                                                       phenotypeId,
+                                                       variantId,
+                                                       datasetId = "gtex_v8") {
+  result <- gtex_query("association/dynsqtl", return_raw = TRUE)
+  result$data <- list(tibble::tibble(data = as.numeric(result$data)))
+  result$genotypes <- list(tibble::tibble(genotypes = as.integer(result$genotypes)))
+
+  result <- tibble::as_tibble(result)
+
+  return(result)
+}

R/gtexr_arguments.R

@@ -55,6 +55,9 @@
 #'   "pancreatitis", "pigment", "pneumonia", "post_menopausal", "prostatitis",
 #'   "saponification", "scarring", "sclerotic", "solar_elastosis",
 #'   "spermatogenesis", "steatosis", "sweat_glands", "tma".
+#' @param phenotypeId String. See
+#'   [GTEx portal FAQs](https://www.gtexportal.org/home/faq#splicingPhenotypeId)
+#'   for further details.
 #' @param pos Integer, vector.
 #' @param project_id String. Options: "gtex", "adult-gtex", "egtex".
 #' @param rin Integer vector.
@@ -123,6 +126,7 @@ gtexr_arguments <- function() {
     "organizationName", "character", TRUE, FALSE, "selectInput", c("GTEx Consortium", "Kid's First"),
     "page", "integer", TRUE, FALSE, "numericInput", c(0, 1000000),
     "pathCategory", "character", FALSE, FALSE, "selectInput", c("adenoma", "amylacea", "atelectasis", "atherosclerosis", "atherosis", "atrophy", "calcification", "cirrhosis", "clean_specimens", "congestion", "corpora_albicantia", "cyst", "desquamation", "diabetic", "dysplasia", "edema", "emphysema", "esophagitis", "fibrosis", "gastritis", "glomerulosclerosis", "goiter", "gynecomastoid", "hashimoto", "heart_failure_cells", "hemorrhage", "hepatitis", "hyalinization", "hypereosinophilia", "hyperplasia", "hypertrophy", "hypoxic", "infarction", "inflammation", "ischemic_changes", "macrophages", "mastopathy", "metaplasia", "monckeberg", "necrosis", "nephritis", "nephrosclerosis", "no_abnormalities", "nodularity", "pancreatitis", "pigment", "pneumonia", "post_menopausal", "prostatitis", "saponification", "scarring", "sclerotic", "solar_elastosis", "spermatogenesis", "steatosis", "sweat_glands", "tma"),
+    "phenotypeId", "character", TRUE, FALSE, "textInput", NA,
     "pos", "integer", FALSE, FALSE, "numericInput", c(0, 248945542),
     "project_id", "character", TRUE, FALSE, "selectInput", c("gtex", "adult-gtex", "egtex"),
     "rin", "integer", FALSE, FALSE, "numericInput", c(-1e8L, 1e8L),

R/validate_args.R

@@ -2,7 +2,7 @@ validate_args <- function(arguments,
                           call) {
   metadata <- gtexr_arguments()
 
-  # TODO move checks for missing args here, and also any "" values e.g. calculate_eqtls(tissueSiteDetailId = "Whole_Blood",
+  # TODO move checks for missing args here, and also any "" values e.g. calculate_expression_quantitative_trait_loci(tissueSiteDetailId = "Whole_Blood",
                    # gencodeId = "",
                    # variantId = "rs79641866")
 

inst/app/app.R

@@ -123,7 +123,7 @@ endpointUI <- function(id, gtexr_fn, gtexr_arguments_metadata, gtexr_functions_m
   gtexr_fn_args <- get_gtexr_fn_args(gtexr_fn)
   gtexr_fn_metadata <- gtexr_functions_metadata[gtexr_functions_metadata$fn_name == gtexr_fn, ]
 
-  # if (gtexr_fn == "calculate_eqtls") {
+  # if (gtexr_fn == "calculate_expression_quantitative_trait_loci") {
   #   browser()
   # }