From 9ee48e3b21bde3a3f51a5922cd51af322f234815 Mon Sep 17 00:00:00 2001
From: Goralsth <thomas.goralski@vai.edu>
Date: Sun, 28 Nov 2021 14:47:18 -0500
Subject: [PATCH] Fixed issue with uninstalled packages Added comments on
 status of TET2 mutations as inducing global hypermethylation phenotype

---
 vignettes/TET2.Rmd | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/vignettes/TET2.Rmd b/vignettes/TET2.Rmd
index a79f410..4299072 100644
--- a/vignettes/TET2.Rmd
+++ b/vignettes/TET2.Rmd
@@ -10,6 +10,17 @@ vignette: >
   %\VignetteEngine{knitr::rmarkdown}
   \usepackage[utf8]{inputenc}
 ---
+```{r}
+if (!require("GEOquery")) {
+  BiocManager::install("GEOquery")
+  library(GEOquery)
+}
+
+if(!require("limma")) {
+  BiocManager::install("limma")
+  library(limma)
+}
+```
 
 ```{r setup, include=FALSE}
 knitr::opts_chunk$set(echo = TRUE)
@@ -151,3 +162,9 @@ fit3 <- eBayes(lmFit(exprs(DNAme)[, as.integer(rownames(design3))], design3))
 # 10 probes for TET2:purity
 
 ```
+It would seem tet2 and IDH mutations occur exclusively. As a result of the number of methylated sites for IDH Mutations vs. tet2 mutations, tet2 does not convincingly contribute to a global hypermethylation phenotype.
+
+
+
+
+