From a1cc7ee33d6c2e1039f33098680bd527620c7701 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Tue, 23 Jun 2020 12:19:26 +0100
Subject: [PATCH] further tidy for OR calcs

---
 scripts/af_or_calcs_scratch.R | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/scripts/af_or_calcs_scratch.R b/scripts/af_or_calcs_scratch.R
index a4b02e2..aadc635 100644
--- a/scripts/af_or_calcs_scratch.R
+++ b/scripts/af_or_calcs_scratch.R
@@ -554,5 +554,12 @@ for (i in snps){
   
   
  # https://stats.stackexchange.com/questions/259635/what-is-the-difference-using-a-fishers-exact-test-vs-a-logistic-regression-for
-  exact2x2(table(dst, mut),tsmethod="central")
+  #mymethod = "minlike" # default
+  mymethod = "central"
+  #mymethod = "blaker"
+  
+  exact2x2(table(dst, mut),tsmethod=mymethod)
+  
+  mcnemar.exact(x,y=NULL, conf.level=.95)
+  
 #=====================================================================