From 22b3aed2fd3fcfd003d58030ec9f5a4bc8230644 Mon Sep 17 00:00:00 2001
From: lcolladotor <lcolladotor@gmail.com>
Date: Wed, 23 Aug 2023 16:31:00 -0400
Subject: [PATCH] Compute some numbers for the pairwise FDR < 0.1 genes

---
 code/05_deploy_app_wholegenome/app.R | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/code/05_deploy_app_wholegenome/app.R b/code/05_deploy_app_wholegenome/app.R
index ae34c7c..d90adad 100644
--- a/code/05_deploy_app_wholegenome/app.R
+++ b/code/05_deploy_app_wholegenome/app.R
@@ -40,6 +40,23 @@ sig_genes <- sig_genes_extract_all(
     sce_layer = sce_pseudo
 )
 
+if (FALSE) {
+    ## Get pairwise numbers for the manuscript
+    pair <- subset(sig_genes, model_type == "pairwise" & fdr < 0.1)
+    pair$combination <-
+        paste0(pair$ensembl, "_", sapply(strsplit(pair$test, "-"), function(x) {
+            paste0(sort(x), collapse = "_")
+        }))
+    pair <- pair[!duplicated(pair$combination), ]
+    table(pair$test)
+    # Ab-n_Ab   Ab-n_both   n_Ab-both n_Ab-n_both n_Ab-n_pTau   n_Ab-pTau   none-n_Ab
+    #     297           1         187         112          39         301         299
+    nrow(pair)
+    # [1] 1236
+    length(unique(pair$ensembl))
+    # [1] 610
+}
+
 ## Extract FDR < 5%
 ## From
 ## https://github.com/LieberInstitute/brainseq_phase2/blob/be2b7f972bb2a0ede320633bf06abe1d4ef2c067/supp_tabs/create_supp_tables.R#L173-L181