add genocode id computation

analyses/AnnotateMergedTable.R

@@ -830,14 +830,22 @@ hpo_gene_list_symptome_groups_summarized_for_join <- hpo_gene_list_symptome_grou
 # TODO: annotate StringDB interactions with strong evidence kidney genes
 # use download tables: https://string-db.org/cgi/download?sessionId=bVJC28yKCRz5&species_text=Homo+sapiens
 # eg physical: https://stringdb-downloads.org/download/protein.physical.links.v12.0/9606.protein.physical.links.v12.0.txt.gz
-# sum the interactions for each gene with the high evidence list, the percentile normalize, additionally show a sting with interacting genes and scores
+# sum the interactions for each gene with the high evidence list, the percentile normalize, additionally show a string with interacting genes and scores
 ############################################
 
 
 ############################################
 # TODO: move this to HGNC table
 # TODO: annotate GTEx kidney expression
 # use https://gtexportal.org/api/v2/redoc#tag/GTEx-Portal-API-Info
+
+# Endpoint to use: 
+# https://gtexportal.org/api/v2/expression/medianGeneExpression?gencodeId=ENSG00000008710.19&gencodeId=ENSG00000203782.5
+# we need enseble gene ids with version
+
+
+
+
 # see GitHub issue for cutoffs
 # TODO: maybe add expression in embryonic kidney from somewhere (e.g. https://descartes.brotmanbaty.org/)
 # descartes: https://atlas.fredhutch.org/data/bbi/descartes/human_gtex/tables/tissue_tpm/kidney.csv (this one for TPM)

analyses/functions/gtex-functions.R

@@ -2,7 +2,7 @@ require(httr)
 require(jsonlite)
 require(tidyverse)
 require(purrr)
-
+library(dplyr)
 
 #' Get Median Tissue Expression Levels from GTEx API
 #'
@@ -50,8 +50,8 @@ get_median_tissue_expression <- function(gencode_ids) {
 #' Fetch Median Tissue Expression Levels from GTEx API for Multiple Genes
 #'
 #' This function takes a character vector of GENCODE gene identifiers as input,
-#' splits it into appropriate chunks to fit the API input size limitations, 
-#' makes a GET request for each chunk of gene identifiers to the GTEx API, 
+#' splits it into appropriate chunks to fit the API input size limitations,
+#' makes a GET request for each chunk of gene identifiers to the GTEx API,
 #' and returns the median tissue expression levels as a tibble.
 #'
 #' @param gencode_ids A character vector representing the GENCODE gene identifiers.
@@ -106,7 +106,7 @@ get_multiple_median_tissue_expression <- function(gencode_ids, max_ids_per_reque
 #' }
 #' @export
 get_gencode_ids <- function(gene_symbols) {
-  
+
   # Prepare the API URL
   base_url <- "https://gtexportal.org/api/v2/reference/gene?"
   ids_query <- paste0("geneId=", gene_symbols, collapse = "&")