differential expression analysis added

seanyoon777 · Apr 3, 2023 · d3445c6 · d3445c6
1 parent a7c230c
commit d3445c6
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Showing 16 changed files with 423 additions and 279 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,4 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
diff --git a/exploratory.R b/exploratory.R
diff --git a/exploratory_data.R b/exploratory_data.R
diff --git a/figures_draft/.DS_Store b/figures_draft/.DS_Store
diff --git a/figures_draft/Correlation Network of CSF Proteomes (filtered) V0.png b/figures_draft/Correlation Network of CSF Proteomes (filtered) V0.png
diff --git a/figures_draft/Correlation Network of CSF Proteomes T2 V0.png b/figures_draft/Correlation Network of CSF Proteomes T2 V0.png
diff --git a/figures_draft/Correlation Network of CSF Proteomes V0.png b/figures_draft/Correlation Network of CSF Proteomes V0.png
diff --git a/figures_draft/Correlation Network of plasma Proteomes T2 V0.png b/figures_draft/Correlation Network of plasma Proteomes T2 V0.png
diff --git a/figures_draft/Correlation Network of plasma Proteomes V0.png b/figures_draft/Correlation Network of plasma Proteomes V0.png
diff --git a/figures_draft/Elbow Graph of CSF proteins (filtered) V0.png b/figures_draft/Elbow Graph of CSF proteins (filtered) V0.png
diff --git a/figures_draft/PCA Scree Plot of CSF (filtered) V0.png b/figures_draft/PCA Scree Plot of CSF (filtered) V0.png
diff --git a/figures_draft/PCA Scree Plot of Plasma (filtered) V0.png b/figures_draft/PCA Scree Plot of Plasma (filtered) V0.png
diff --git a/...ft/Prediction of Biological Age using PCA Preprocessed Intake (filtered) V0.png b/...ft/Prediction of Biological Age using PCA Preprocessed Intake (filtered) V0.png
diff --git a/proteomics.R b/proteomics.R
@@ -1,24 +1,18 @@
 #setting foundations
-if(!require(tidyverse)) install.packages("tidyverse", repos = "http://cran.us.r-project.org")
-if(!require(caret)) install.packages("caret", repos = "http://cran.us.r-project.org")
-if(!require(data.table)) install.packages("data.table", repos = "http://cran.us.r-project.org")
-install.packages("corrr")
-install.packages("igraph")
-install.packages('cluster')
-install.packages('factoextra')
-library(corrr)
-library(tidyverse)
-library(purrr)
-library(igraph)
-library(corrplot)
-library(caret)
-library(dplyr)
-library(data.table)
-library(ggplot2)
-library(pls)
-library(tidyverse)
-library(cluster)
-library(factoextra)
+
+load_lib("tidyverse")
+load_lib("caret")
+load_lib("data.table")
+load_lib("corrr")
+load_lib("igraph")
+load_lib("cluster")
+load_lib("factoextra")
+load_lib("purrr")
+load_lib("corrplot")
+load_lib("dplyr")
+load_lib("ggplot2")
+load_lib("pls")
+load_lib("ggraph")
 
 loess_models <- function(plasma_prot_zscore_age, loess_span = 0.75) {
   plasma_long <- plasma_prot_zscore_age %>%
@@ -65,3 +59,9 @@ loess_heatmap <- function(plasma_pred_zscore_long) {
           plot.title = element_text(hjust = 0.5))
 }
 
+
+#cluster by trend 
+
+
+
+
diff --git a/proteomics_project.Rproj b/proteomics_project.Rproj
@@ -0,0 +1,13 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX