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Fixed issue with uninstalled packages #5

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Fixed issue with uninstalled packages #5

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17 changes: 17 additions & 0 deletions vignettes/TET2.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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.