From ec9177e48620d31c634e9459e8c54bd59968e402 Mon Sep 17 00:00:00 2001
From: Svad98 <91341854+Svad98@users.noreply.github.com>
Date: Sat, 27 Nov 2021 14:49:25 -0500
Subject: [PATCH 01/12] added my name as reviewer

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

diff --git a/vignettes/TET2.Rmd b/vignettes/TET2.Rmd
index a79f410..ed40adc 100644
--- a/vignettes/TET2.Rmd
+++ b/vignettes/TET2.Rmd
@@ -1,6 +1,7 @@
 ---
 title: "Code review: TET2 and hypermethylation"
 author: "Tim Triche"
+reviewer: "Svetlana Djirackor"
 date: "November 22nd, 2021"
 output: 
   html_document:

From ede2246b41fcd131c4f32c1058adee34cead6b91 Mon Sep 17 00:00:00 2001
From: Svad98 <91341854+Svad98@users.noreply.github.com>
Date: Sat, 27 Nov 2021 14:52:57 -0500
Subject: [PATCH 02/12] info about load_all - necessary for code to run

---
 vignettes/TET2.Rmd | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/vignettes/TET2.Rmd b/vignettes/TET2.Rmd
index ed40adc..45e7ca2 100644
--- a/vignettes/TET2.Rmd
+++ b/vignettes/TET2.Rmd
@@ -16,7 +16,8 @@ vignette: >
 knitr::opts_chunk$set(echo = TRUE)
 knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
 library(devtools)
-load_all("./")
+load_all("./") 
+# the load_all("./") is necessary to make the code run (DNAme does not work without it)
 ```
 
 # Installation

From 2bd2e6a5b93d9e0ed16f85bde8a81b8c0de95753 Mon Sep 17 00:00:00 2001
From: Svad98 <91341854+Svad98@users.noreply.github.com>
Date: Sat, 27 Nov 2021 17:03:01 -0500
Subject: [PATCH 03/12] answer for mutual exclusivity of IDH and TET2

---
 vignettes/TET2.Rmd | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/vignettes/TET2.Rmd b/vignettes/TET2.Rmd
index 45e7ca2..ce19304 100644
--- a/vignettes/TET2.Rmd
+++ b/vignettes/TET2.Rmd
@@ -88,6 +88,8 @@ dim(DNAme)
 
 Is it the case that TET2, IDH1, and IDH2 mutations are exclusive?
 
+With the exception of GSM604380/patient 316, TET2 and IDH1/2 mutations are exclusive.
+
 ```{r, heatmap, eval=TRUE}
 
 # always plot your data

From 65f1094bd3c095d9c90d1a1c11e6c83f34c0d784 Mon Sep 17 00:00:00 2001
From: Svad98 <91341854+Svad98@users.noreply.github.com>
Date: Sun, 28 Nov 2021 15:31:19 -0500
Subject: [PATCH 04/12] Finding out who the anomaly is - could be useful later

---
 vignettes/TET2.Rmd | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/vignettes/TET2.Rmd b/vignettes/TET2.Rmd
index ce19304..a3e5433 100644
--- a/vignettes/TET2.Rmd
+++ b/vignettes/TET2.Rmd
@@ -87,8 +87,7 @@ dim(DNAme)
 ### Some contrasts
 
 Is it the case that TET2, IDH1, and IDH2 mutations are exclusive?
-
-With the exception of GSM604380/patient 316, TET2 and IDH1/2 mutations are exclusive.
+_With the exception of GSM604380/patient 316, TET2 and IDH1/2 mutations are exclusive._
 
 ```{r, heatmap, eval=TRUE}
 
@@ -100,6 +99,21 @@ Heatmap(mutations, col=c("lightgray","darkred"), name="mutant", column_km=4,
 
 ```
 
+### Healthy curiosity
+```{r, The OddBall}
+# one patient is the odd-ball here
+as_tibble(DNAme$`idh1.idh2:ch1`) -> idh1_idh2
+# since there is ch1 and 2, I compared both and they have the exact same information
+# as_tibble(DNAme$`idh1.idh2:ch2`) -> idh1_idh2_next
+# idh1_idh2 == idh1_idh2_next - returns TRUE
+as_tibble(DNAme$`tet2:ch1`) -> tet
+# as_tibble(DNAme$`tet2:ch2`) -> tet_2
+# tet == tet_2 - returns TRUE
+colnames(tet) <- c("TET")
+colnames(idh1_idh2) <- c("IDH")
+compiled <- cbind(tet, idh1_idh2)
+View(compiled) # scrolled through and identified the patient/sample number that had the mutations in both TET2 and IDH
+```
 Do we see genome-wide hypermethylation from TET2 mutations? 
 
 ```{r, TET2_vs_IDH}

From adc74535618a542933605b5cc72a081334184a08 Mon Sep 17 00:00:00 2001
From: Svad98 <91341854+Svad98@users.noreply.github.com>
Date: Sun, 28 Nov 2021 15:35:18 -0500
Subject: [PATCH 05/12] what does this chunk show us about GWMe?

---
 vignettes/TET2.Rmd | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/vignettes/TET2.Rmd b/vignettes/TET2.Rmd
index a3e5433..5d60d8d 100644
--- a/vignettes/TET2.Rmd
+++ b/vignettes/TET2.Rmd
@@ -114,6 +114,7 @@ colnames(idh1_idh2) <- c("IDH")
 compiled <- cbind(tet, idh1_idh2)
 View(compiled) # scrolled through and identified the patient/sample number that had the mutations in both TET2 and IDH
 ```
+
 Do we see genome-wide hypermethylation from TET2 mutations? 
 
 ```{r, TET2_vs_IDH}
@@ -169,3 +170,9 @@ fit3 <- eBayes(lmFit(exprs(DNAme)[, as.integer(rownames(design3))], design3))
 # 10 probes for TET2:purity
 
 ```
+
+I'm unsure of how to interpret the code above:
+- The annotation/description of the designs are unclear. 
+- Why would we run the code this way?
+- What do the probe numbers mean?
+- How can this be translated into assessing genome-wide methylation?

From dfd5a90defcc1e9fef02d8eeba0b85287a60a2ca Mon Sep 17 00:00:00 2001
From: Svad98 <91341854+Svad98@users.noreply.github.com>
Date: Sun, 28 Nov 2021 15:38:51 -0500
Subject: [PATCH 06/12] need this for chunk to run

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

diff --git a/vignettes/TET2.Rmd b/vignettes/TET2.Rmd
index 5d60d8d..c6a5002 100644
--- a/vignettes/TET2.Rmd
+++ b/vignettes/TET2.Rmd
@@ -101,6 +101,7 @@ Heatmap(mutations, col=c("lightgray","darkred"), name="mutant", column_km=4,
 
 ### Healthy curiosity
 ```{r, The OddBall}
+library(tidyverse)
 # one patient is the odd-ball here
 as_tibble(DNAme$`idh1.idh2:ch1`) -> idh1_idh2
 # since there is ch1 and 2, I compared both and they have the exact same information

From f0992f547ca1cda6ac6d418ad2c275d3bbfa954e Mon Sep 17 00:00:00 2001
From: Svad98 <91341854+Svad98@users.noreply.github.com>
Date: Sun, 28 Nov 2021 15:43:59 -0500
Subject: [PATCH 07/12] i'm the reviewer

---
 vignettes/TET2.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vignettes/TET2.Rmd b/vignettes/TET2.Rmd
index c6a5002..279e6d8 100644
--- a/vignettes/TET2.Rmd
+++ b/vignettes/TET2.Rmd
@@ -1,7 +1,6 @@
 ---
 title: "Code review: TET2 and hypermethylation"
 author: "Tim Triche"
-reviewer: "Svetlana Djirackor"
 date: "November 22nd, 2021"
 output: 
   html_document:
@@ -19,6 +18,7 @@ library(devtools)
 load_all("./") 
 # the load_all("./") is necessary to make the code run (DNAme does not work without it)
 ```
+# Reviewed by Svetlana Djirackor
 
 # Installation
 

From e0857ec72e4b9511cd6f84287e92876f3ddc2315 Mon Sep 17 00:00:00 2001
From: Svad98 <91341854+Svad98@users.noreply.github.com>
Date: Sun, 28 Nov 2021 18:30:21 -0500
Subject: [PATCH 08/12] Revert "Sveta's Edits"

---
 vignettes/TET2.Rmd | 28 +---------------------------
 1 file changed, 1 insertion(+), 27 deletions(-)

diff --git a/vignettes/TET2.Rmd b/vignettes/TET2.Rmd
index 279e6d8..a79f410 100644
--- a/vignettes/TET2.Rmd
+++ b/vignettes/TET2.Rmd
@@ -15,10 +15,8 @@ vignette: >
 knitr::opts_chunk$set(echo = TRUE)
 knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
 library(devtools)
-load_all("./") 
-# the load_all("./") is necessary to make the code run (DNAme does not work without it)
+load_all("./")
 ```
-# Reviewed by Svetlana Djirackor
 
 # Installation
 
@@ -87,7 +85,6 @@ dim(DNAme)
 ### Some contrasts
 
 Is it the case that TET2, IDH1, and IDH2 mutations are exclusive?
-_With the exception of GSM604380/patient 316, TET2 and IDH1/2 mutations are exclusive._
 
 ```{r, heatmap, eval=TRUE}
 
@@ -99,23 +96,6 @@ Heatmap(mutations, col=c("lightgray","darkred"), name="mutant", column_km=4,
 
 ```
 
-### Healthy curiosity
-```{r, The OddBall}
-library(tidyverse)
-# one patient is the odd-ball here
-as_tibble(DNAme$`idh1.idh2:ch1`) -> idh1_idh2
-# since there is ch1 and 2, I compared both and they have the exact same information
-# as_tibble(DNAme$`idh1.idh2:ch2`) -> idh1_idh2_next
-# idh1_idh2 == idh1_idh2_next - returns TRUE
-as_tibble(DNAme$`tet2:ch1`) -> tet
-# as_tibble(DNAme$`tet2:ch2`) -> tet_2
-# tet == tet_2 - returns TRUE
-colnames(tet) <- c("TET")
-colnames(idh1_idh2) <- c("IDH")
-compiled <- cbind(tet, idh1_idh2)
-View(compiled) # scrolled through and identified the patient/sample number that had the mutations in both TET2 and IDH
-```
-
 Do we see genome-wide hypermethylation from TET2 mutations? 
 
 ```{r, TET2_vs_IDH}
@@ -171,9 +151,3 @@ fit3 <- eBayes(lmFit(exprs(DNAme)[, as.integer(rownames(design3))], design3))
 # 10 probes for TET2:purity
 
 ```
-
-I'm unsure of how to interpret the code above:
-- The annotation/description of the designs are unclear. 
-- Why would we run the code this way?
-- What do the probe numbers mean?
-- How can this be translated into assessing genome-wide methylation?

From df96c208369b68aa1392ff6608834ae622ce6b2c Mon Sep 17 00:00:00 2001
From: ShantiniqueMiller <shantiniquemiller40@gmail.com>
Date: Mon, 29 Nov 2021 12:06:59 -0500
Subject: [PATCH 09/12] Complete

---
 .gitignore                     | 12 +-----------
 WorldsSimplestCodeReview.Rproj | 17 +++++++++++++++++
 vignettes/TET2.Rmd             |  1 +
 vignettes/TET2.md              | 13 +++++++++++--
 4 files changed, 30 insertions(+), 13 deletions(-)
 create mode 100644 WorldsSimplestCodeReview.Rproj

diff --git a/.gitignore b/.gitignore
index fae8299..8ab3dbb 100644
--- a/.gitignore
+++ b/.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
diff --git a/WorldsSimplestCodeReview.Rproj b/WorldsSimplestCodeReview.Rproj
new file mode 100644
index 0000000..21a4da0
--- /dev/null
+++ b/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
diff --git a/vignettes/TET2.Rmd b/vignettes/TET2.Rmd
index a79f410..1eefee3 100644
--- a/vignettes/TET2.Rmd
+++ b/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)
diff --git a/vignettes/TET2.md b/vignettes/TET2.md
index 1f63bef..d4895e1 100644
--- a/vignettes/TET2.md
+++ b/vignettes/TET2.md
@@ -1,3 +1,4 @@
+#Did not run these.
 ---
 title: "Code review: TET2 and hypermethylation"
 author: "Tim Triche"
@@ -12,12 +13,13 @@ 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")
@@ -25,6 +27,7 @@ Install the WorldsSimplestCodeReview package, if you haven't.
 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:

From da94736d1e08d9f78a16a448d032d1e43b6fea83 Mon Sep 17 00:00:00 2001
From: Christina Straham <Christina-Straham@github.com>
Date: Mon, 29 Nov 2021 12:09:45 -0500
Subject: [PATCH 10/12] I only changed the font size for the heat map and added
 some comments!

---
 vignettes/TET2.Rmd | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/vignettes/TET2.Rmd b/vignettes/TET2.Rmd
index a79f410..935a468 100644
--- a/vignettes/TET2.Rmd
+++ b/vignettes/TET2.Rmd
@@ -16,6 +16,7 @@ knitr::opts_chunk$set(echo = TRUE)
 knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
 library(devtools)
 load_all("./")
+# not sure what this is for but it is important. When this chunk is ran, a pretty Rmd is pulled up of the code.
 ```
 
 # Installation
@@ -34,6 +35,8 @@ To extract just the R code, you can use knitr::knit(input, tangle=TRUE):
 ```{r, tangle, eval = FALSE, message = FALSE, echo = FALSE}
 # knitr::knit("TET2.Rmd", tangle = TRUE) 
 # [1] "TET2.R"
+
+#What is the point of this chunk?
 ```
 
 # Introduction
@@ -92,7 +95,7 @@ Is it the case that TET2, IDH1, and IDH2 mutations are exclusive?
 library(ComplexHeatmap)
 mutations <- t(as.matrix(pData(DNAme)[, c("TET2", "IDH")]))
 Heatmap(mutations, col=c("lightgray","darkred"), name="mutant", column_km=4,
-        column_names_gp = gpar(fontsize = 7))
+        column_names_gp = gpar(fontsize = 0))
 
 ```
 
@@ -111,6 +114,8 @@ fit1 <- eBayes(lmFit(exprs(DNAme), design1))
                                            coef=grep("IDH", colnames(design1)), 
                                            p.value=0.05, # change if you like 
                                            number=Inf)))
+#if you're having trouble running this entire chunk or receiving error "'pData': object 'DNAme' not found", run design1 chunk of code first and the rest of the chunk should follow suit. I don't know why that is or if it is just me.
+
 # 6513 probes for IDH
 
 (TET_diffmeth_probes_fit1 <- nrow(topTable(fit1, 
@@ -126,6 +131,7 @@ fit2 <- eBayes(lmFit(exprs(DNAme), design2))
                                            coef=grep("IDH", colnames(design2)), 
                                            p.value=0.05, # change if you like 
                                            number=Inf)))
+
 # 6651 probes for IDH 
 
 (TET2_diffmeth_probes_fit2 <- nrow(topTable(fit2, 

From 3c5f902efe6866ff4bc72061b2769d39c534a4b4 Mon Sep 17 00:00:00 2001
From: ShantiniqueMiller <92749036+ShantiniqueMiller@users.noreply.github.com>
Date: Mon, 29 Nov 2021 12:16:19 -0500
Subject: [PATCH 11/12] Update TET2.Rmd

Conclusions drawn
---
 vignettes/TET2.Rmd | 1 +
 1 file changed, 1 insertion(+)

diff --git a/vignettes/TET2.Rmd b/vignettes/TET2.Rmd
index 1eefee3..13b9028 100644
--- a/vignettes/TET2.Rmd
+++ b/vignettes/TET2.Rmd
@@ -152,3 +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. 

From 48c00ba228f96f299546034dd5810f4fe81db75d Mon Sep 17 00:00:00 2001
From: kate-t-48 <67631404+kate-t-48@users.noreply.github.com>
Date: Mon, 29 Nov 2021 12:37:36 -0500
Subject: [PATCH 12/12] Revert "I only changed the font size for the heat map
 and added some comments!"

---
 vignettes/TET2.Rmd | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/vignettes/TET2.Rmd b/vignettes/TET2.Rmd
index c6119ee..13b9028 100644
--- a/vignettes/TET2.Rmd
+++ b/vignettes/TET2.Rmd
@@ -16,7 +16,6 @@ knitr::opts_chunk$set(echo = TRUE)
 knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
 library(devtools)
 load_all("./")
-# not sure what this is for but it is important. When this chunk is ran, a pretty Rmd is pulled up of the code.
 ```
 
 # Installation
@@ -35,8 +34,6 @@ To extract just the R code, you can use knitr::knit(input, tangle=TRUE):
 ```{r, tangle, eval = FALSE, message = FALSE, echo = FALSE}
 # knitr::knit("TET2.Rmd", tangle = TRUE) 
 # [1] "TET2.R"
-
-#What is the point of this chunk?
 ```
 
 # Introduction
@@ -96,7 +93,7 @@ Is it the case that TET2, IDH1, and IDH2 mutations are exclusive?
 library(ComplexHeatmap)
 mutations <- t(as.matrix(pData(DNAme)[, c("TET2", "IDH")]))
 Heatmap(mutations, col=c("lightgray","darkred"), name="mutant", column_km=4,
-        column_names_gp = gpar(fontsize = 0))
+        column_names_gp = gpar(fontsize = 7))
 
 ```
 
@@ -115,8 +112,6 @@ fit1 <- eBayes(lmFit(exprs(DNAme), design1))
                                            coef=grep("IDH", colnames(design1)), 
                                            p.value=0.05, # change if you like 
                                            number=Inf)))
-#if you're having trouble running this entire chunk or receiving error "'pData': object 'DNAme' not found", run design1 chunk of code first and the rest of the chunk should follow suit. I don't know why that is or if it is just me.
-
 # 6513 probes for IDH
 
 (TET_diffmeth_probes_fit1 <- nrow(topTable(fit1, 
@@ -132,7 +127,6 @@ fit2 <- eBayes(lmFit(exprs(DNAme), design2))
                                            coef=grep("IDH", colnames(design2)), 
                                            p.value=0.05, # change if you like 
                                            number=Inf)))
-
 # 6651 probes for IDH 
 
 (TET2_diffmeth_probes_fit2 <- nrow(topTable(fit2,