20240922 release

sigven · Sep 24, 2024 · 133885f · 133885f
1 parent 73f809b
commit 133885f
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Showing 3 changed files with 13 additions and 3 deletions.
diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/data-raw/data-raw.R b/data-raw/data-raw.R
@@ -6,8 +6,8 @@ source("data-raw/gwas_utils.R")
 
 options(timeout = 500000)
 
-catalog_version_date <- '2024-08-12'
-ebi_catalog_version_date <- '20240812'
+catalog_version_date <- '2024-09-22'
+ebi_catalog_version_date <- '20240922'
 fname_catalog_associations <- 
   file.path(
     "data-raw", 
@@ -188,7 +188,7 @@ for (c in gwas_collections) {
   gwas_phenotype_records <- as.data.frame(
     gwas_hits[[c]] |>
       dplyr::left_join(
-        gwas_citations[[c]],
+        gwas_citations[[c]], by = "pmid",
         relationship = "many-to-many") |>
       dplyr::mutate(gwas_catalog_version = ebi_catalog_version_date) |>
       dplyr::mutate(p_value_verbose = sprintf("%2.1e",p_value)) |>

diff --git a/data-raw/gwas_utils.R b/data-raw/gwas_utils.R
@@ -7,6 +7,16 @@
 #' 
 get_dbsnp_data <- function(rsids, cache_dbsnp_fname = NA){
 
+  # gw_hits <- gwas_hits_pr_rsid$cancer |>
+  #   dplyr::filter(
+  #     stringr::str_detect(rsid, "^rs[0-9]{1,}")) |>
+  #   tidyr::separate(
+  #     gwas_hit,
+  #     c("rsid","risk_allele","pmid","tag","p_value","efo_id"),
+  #     sep = "\\|"
+  #   )
+
+  rsids <- rsids[stringr::str_detect(rsids,"^rs[0-9]{1,}")]
   rsid_df <- data.frame('rsid' = rsids)
   cache_dbsnp <- data.frame()