Create composition_analysis.R

mcrewcow · Dec 5, 2023 · 383ce84 · 383ce84
1 parent d003ead
commit 383ce84
Showing 1 changed file with 17 additions and 0 deletions.
diff --git a/composition_analysis.R b/composition_analysis.R
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+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)