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Scripts/Script11.R

+######################################################################################################################################################################################################
+anchor_breast<-read.csv("./Tables/Table10.csv")$Gene 
+anchor_colorectal<-read.csv("./Tables/Table11.csv")$Gene
+Candidate_Breast<-read.csv("./Tables/Table8.csv")$x
+Candidate_Colorectal<-read.csv("./Tables/Table9.csv")$x
+######################################################################################################################################################################################################
+GlobalESS<-readRDS("./SupplementaryData/SupplementaryData2/Global_ess_corr.rds")
+Edges<-readRDS("./SupplementaryData/SupplementaryData2/EDGES.rds")
+######################################################################################################################################################################################################
+#Breast
+coessential_breast2<-list()
+all_coess_breast2<-c()
+
+for (i in 1:40){
+  print(i)
+  set1<-which(Edges$from==as.character(anchor_breast[i]))
+  set2<-which(Edges$dashes==FALSE)
+  set3<-union(which(Edges$modified_effector=="Mutation"),which(Edges$modified_effector=="Expression"))
+  set4<-union(which(Edges$comparision_in=="Breast Cancer"),which(Edges$comparision_in=="Breast"))
+  set5<-intersect(which(Edges$Confidence=="Group A"),which(Edges$width>1))
+  set6<-intersect(which(Edges$median_group>0.5),which(Edges$median_group>Edges$median_other))
+  selected<-intersect(intersect(intersect(set1,set2),intersect(set3,set4)),intersect(set5,set6))
+  coessential_breast2[[i]]<-unique(Edges$to[selected])
+  all_coess_breast2<-c(all_coess_breast2,coessential_breast2[[i]])
+}
+all_coess_breast2<-unique(all_coess_breast2)
+all_coess_breast2<-intersect(Candidate_Breast,all_coess_breast2)
+
+#Colorectal
+coessential_colorectal2<-list()
+all_coess_colorectal2<-c()
+for (i in 1:43){
+  print(i)
+  set1<-which(Edges$from==as.character(anchor_colorectal[i]))
+  set2<-which(Edges$dashes==FALSE)
+  set3<-union(which(Edges$modified_effector=="Mutation"),which(Edges$modified_effector=="Expression"))
+  set4<-union(which(Edges$comparision_in=="Colorectal Cancer"),which(Edges$comparision_in=="Colon/Rectum"))
+  set5<-intersect(which(Edges$Confidence=="Group A"),which(Edges$width>1))
+  set6<-intersect(which(Edges$median_group>0.5),which(Edges$median_group>Edges$median_other))
+  selected<-intersect(intersect(intersect(set1,set2),intersect(set3,set4)),intersect(set5,set6))
+  coessential_colorectal2[[i]]<-unique(Edges$to[selected])
+  all_coess_colorectal2<-c(all_coess_colorectal2,coessential_colorectal2[[i]])
+}
+all_coess_colorectal2<-unique(all_coess_colorectal2)
+all_coess_colorectal2<-intersect(Colorectal_Genes,all_coess_colorectal2)
+