From 383ce8407750ff07326c2b8499052caf927cd442 Mon Sep 17 00:00:00 2001
From: Emil Kriukov <77118598+mcrewcow@users.noreply.github.com>
Date: Tue, 5 Dec 2023 17:11:14 -0500
Subject: [PATCH] Create composition_analysis.R

---
 composition_analysis.R | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 composition_analysis.R

diff --git a/composition_analysis.R b/composition_analysis.R
new file mode 100644
index 0000000..ae925fd
--- /dev/null
+++ b/composition_analysis.R
@@ -0,0 +1,17 @@
+library(scDC)
+exprsMat <- GetAssayData(object = lydia, assay = "RNA", slot = "data")
+cellTypes <- lydia$anno2
+subject <- lydia$background
+cond <- lydia$background
+dim(exprsMat)
+table(subject, cellTypes)
+table(cond, cellTypes)
+res_scDC_noClust <- scDC_noClustering(cellTypes, subject, calCI = TRUE, 
+                                      calCI_method = c("percentile", "BCa", "multinom"),
+                                      nboot = 50)
+barplotCI(res_scDC_noClust, c("WT","DFcKO"))
+densityCI(res_scDC_noClust, c("WT",'DFcKO'))
+res_GLM <- fitGLM(res_scDC_noClust, c("WT",'DFcKO'), 
+                  pairwise = T)
+summary(res_GLM$pool_res_fixed)
+summary(res_GLM$pool_res_random)