Revert "I only changed the font size for the heat map and added some comments!"

.gitignore

@@ -1,39 +1,29 @@
 # History files
 .Rhistory
 .Rapp.history
-
 # Session Data files
 .RData
-
 # User-specific files
 .Ruserdata
-
 # Example code in package build process
 *-Ex.R
-
 # Output files from R CMD build
 /*.tar.gz
-
 # Output files from R CMD check
 /*.Rcheck/
-
 # RStudio files
 .Rproj.user/
-
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf
-
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
-
 # knitr and R markdown default cache directories
 *_cache/
 /cache/
-
 # Temporary files created by R markdown
 *.utf8.md
 *.knit.md
-
 # R Environment Variables
 .Renviron
+.Rbuildignore

WorldsSimplestCodeReview.Rproj

@@ -0,0 +1,17 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

vignettes/TET2.Rmd

@@ -53,6 +53,7 @@ Some of you who have seen volcano plots before can guess where this is going.
 
 ```{r, fetchGEO}
 
+install.packages(lima)
 library(limma)
 library(GEOquery)
 if (!exists("DNAme")) data(DNAme)
@@ -151,3 +152,4 @@ fit3 <- eBayes(lmFit(exprs(DNAme)[, as.integer(rownames(design3))], design3))
 # 10 probes for TET2:purity
 
 ```
+IDH and TET2 are mutually exclusive as indicative by the probe numbers.There is a vast difference in probe number values for both with IDH >5000 and TET2 <10. This also aligns with the conclusions derived from the paper. Therefore, I would say the the codes were able to prove the points that they were trying to make about mutual exclusiveness of the genes. The part that remains a bit unclear is how exactly does this tie into genome wide hypermethylation. 

vignettes/TET2.md

@@ -1,3 +1,4 @@
+#Did not run these.
 ---
 title: "Code review: TET2 and hypermethylation"
 author: "Tim Triche"
@@ -12,19 +13,21 @@ vignette: >
 ---
 
 
+#Start code running here!!!
 
-# Installation
+# First:Installation
 
 Install the WorldsSimplestCodeReview package, if you haven't. 
 
-
+#Install these packages and run code w/o hashtag
 ```r
 #install.packages("remotes")
 #install.packages("BiocManager")
 #BiocManager::install("VanAndelInstitute/WorldsSimplestCodeReview")
 library(knitr)
 ```
 
+#This code reads an error, requires additional? When ran, a '+' sign is added to next line. Excluded this code as a result.To remove lus sign hit "ESC" 
 To extract just the R code, you can use knitr::knit(input, tangle=TRUE):
 
 
@@ -48,13 +51,19 @@ Some of you who have seen volcano plots before can guess where this is going.
 ```r
 
 library(limma)
+
+
 library(GEOquery)
+
+#DName not found, showed up as warning message
 if (!exists("DNAme")) data(DNAme)
 
+
 if (FALSE) { # this takes about 5 minutes:
 
   # needed to fetch data
   library(GEOquery) 
+  install
   MSK_HOVON <- getGEO("GSE24505")
 
   # skip the expression data: