Commit d9f1fc04 authored by Sayed Rzgar Hosseini's avatar Sayed Rzgar Hosseini
Browse files

Delete Script00.R

parent e7c55266
######################################################################################################################################################################################################Associated_TNBC<-read.csv("/Users/rzgar/Desktop/Research/ENCORE_MEETING/Associated_TNBC.csv")
Associated_Breast<-read.csv("./Tables/Table1.csv") # Original list of Open Targets Associated Breast cancer genes
Associated_Colorectal<-read.csv("./Tables/Table2.csv") # Original list of Open Targets Associated Colorectal cancer genes
Breast_Genes<-Associated_Breast$target.gene_info.symbol
Colorectal_Genes<-Associated_Colorectal$target.gene_info.symbol
######################################################################################################################################################################################################
## Excluding the Core-essential genes
Core_Essential<-read.csv("./Tables/Table5.csv") #List of core essential genes
CORE_ESS<-as.character(Core_Essential$gene[union(union(which(Core_Essential$BAGEL_Essential==TRUE),which(Core_Essential$ADaM_Core==TRUE)),union(which(Core_Essential$STEM_Core==TRUE),which(Core_Essential$Dede_Core==TRUE)))])
Breast_Genes<-setdiff(Breast_Genes,CORE_ESS) #Excluding the core essential genes
Colorectal_Genes<-setdiff(Colorectal_Genes,CORE_ESS) # Excluding the core essential genes
######################################################################################################################################################################################################### Expression Analysis:
## Excluding the non-expressed genes
RNASeq<-read.csv("./Tables/Table3.csv") # Expression profiles of Breast cancer cell lines
RNAval<-apply(matrix(as.numeric(as.matrix(RNASeq[4:37282,3:17])),nrow=37279,ncol=15),1,sum,na.rm=TRUE)
breast_NONexpressed<-as.character(RNASeq[(which(RNAval==0)+3),2])
Breast_Genes<-setdiff(Breast_Genes,breast_NONexpressed)
RNASeq2<-read.csv("./Tables/Table4.csv") # Expression profiles of Colorectal cancer cell lines
colon_NONexpressed<-RNASeq2[which(apply(RNASeq2[,3:27],1,sum,na.rm=TRUE)==0),2]
Colorectal_Genes<-setdiff(Colorectal_Genes,colon_NONexpressed)
######################################################################################################################################################################################################breast_set5.2<-read.csv("/Users/rzgar/Desktop/Research/ENCORE_MEETING/BREAST1/Library_Prep/SET5.2.csv")
## Excluding the Context-specific genes
context_colorectal<-read.csv("./Tables/Table6.csv") # set of context-specific (breast) genes (output of Cen-Tools)
context_breast<-read.csv("./Tables/Table7.csv") # set of context-specific (colorectal) genes (output of Cen-Tools)
Breast_Genes<-setdiff(Breast_Genes,context_breast[,1]) #Excluding the context-specific genes
Colorectal_Genes<-setdiff(Colorectal_Genes,context_colorectal[,1]) #Excluding the context-specific genes
write.csv(Breast_Genes, "./Tables/Table8.csv", append = FALSE, sep = " ", dec = ".",row.names = FALSE, col.names = TRUE) #The final list of candidate breast library genes
write.csv(Colorectal_Genes, "./Tables/Table9.csv", append = FALSE, sep = " ", dec = ".",row.names = FALSE, col.names = TRUE) #The final list of candidate colorectal library genes
######################################################################################################################################################################################################breast_set5.2<-read.csv("/Users/rzgar/Desktop/Research/ENCORE_MEETING/BREAST1/Library_Prep/SET5.2.csv")
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