From 3c96a577bc6154620238fca9de9ddd86775606bf Mon Sep 17 00:00:00 2001
From: Oliver Mazariegos <oliver.mazariegos98@gmail.com>
Date: Sun, 19 Nov 2023 20:52:13 -0500
Subject: [PATCH] feat: retrieving initial information for the dashboard

---
 setup.R | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 setup.R

diff --git a/setup.R b/setup.R
new file mode 100644
index 0000000..b5b9a52
--- /dev/null
+++ b/setup.R
@@ -0,0 +1,41 @@
+library(GenomicDataCommons)
+
+
+projects <- GenomicDataCommons::projects() %>%
+  GenomicDataCommons::filter(program.name == "TCGA") %>%
+  GenomicDataCommons::facet(c("name", "project_id")) %>%
+  results(size = 100)
+
+tcga_project_ids <- projects$project_id
+
+projects_info <- projects() %>%
+  GenomicDataCommons::filter(project_id %in% tcga_project_ids) %>%
+  results_all()
+
+diseases_types <- unique(rapply(projects$disease_type, function(x) head(x, 30)))
+
+primary_sites <- unique(rapply(projects$primary_site, function(x) head(x, 30)))
+
+cases_pre_info <- cases() %>%
+  GenomicDataCommons::filter(project.project_id %in% tcga_project_ids) %>%
+  results_all()
+
+cases_info <- GenomicDataCommons::cases() %>%
+  GenomicDataCommons::filter(project.project_id %in% tcga_project_ids) %>%
+  GenomicDataCommons::facet(c(
+    "project.project_id",
+    "demographic.race",
+    "demographic.gender",
+    "demographic.ethnicity",
+    "demographic.vital_status",
+    "diagnoses.primary_diagnosis",
+    "diagnoses.site_of_resection_or_biopsy",
+    "primary_site"
+  )) %>%
+  aggregations()
+
+
+files_info <- GenomicDataCommons::files() %>%
+  GenomicDataCommons::filter(access == "open") %>%
+  GenomicDataCommons::facet(c("type", "data_type")) %>%
+  aggregations()