Commit 2989f222 authored by Sayed Rzgar Hosseini's avatar Sayed Rzgar Hosseini
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parent 9a61c991
######################################################################################################################################################################################################
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
######################################################################################################################################################################################################
##### Breast ######################################################################################################################################################
A<-character()
B<-character()
# Reading the raw files downloaded from cBioPortal
for (i in 1:9){
A<-c(A,as.character(read.csv(paste0("./SupplementaryData/SupplementaryData3/B/table1.",i,".csv"))$A))
B<-c(B,as.character(read.csv(paste0("./SupplementaryData/SupplementaryData3/B/table1.",i,".csv"))$B))
}
for (i in 1:49){
A<-c(A,as.character(read.csv(paste0("./SupplementaryData/SupplementaryData3/B/table2.",i,".csv"))$A))
B<-c(B,as.character(read.csv(paste0("./SupplementaryData/SupplementaryData3/B/table2.",i,".csv"))$B))
}
BE<-unique(data.frame(A=A,B=B,stringsAsFactors = FALSE))
# Subsetting based on the anchor genes
A<-character()
B<-character()
for (i in 1:dim(BE)[1]){
if ((length(intersect(anchor_breast,BE$A[i]))>0)&&(length(intersect(Candidate_Breast,BE$B[i]))>0)){A<-c(A,BE$A[i]);B<-c(B,BE$B[i])}
else if((length(intersect(anchor_breast,BE$B[i]))>0)&&(length(intersect(Candidate_Breast,BE$A[i]))>0)){A<-c(A,BE$B[i]);B<-c(B,BE$A[i])}
else {}
}
Breast_MUeX<-unique(data.frame(A=A,B=B,stringsAsFactors = FALSE))
Breast_MutualEx_Candidates<-unique(as.character(Breast_MUeX[,2]))# Final list of breast gene candidates based on mutual exclusivity criteria
##### Colorectal ######################################################################################################################################################
A<-character()
B<-character()
# Reading the raw files downloaded from cBioPortal
for (i in 1:17){
A<-c(A,as.character(read.csv(paste0("./SupplementaryData/SupplementaryData3/C/table",i,".csv"))$A))
B<-c(B,as.character(read.csv(paste0("./SupplementaryData/SupplementaryData3/C/table",i,".csv"))$B))
}
CE<-unique(data.frame(A=A,B=B,stringsAsFactors = FALSE))
# Subsetting based on the anchor genes
A<-character()
B<-character()
for (i in 1:dim(CE)[1]){
if ((length(intersect(anchor_colorectal,CE$A[i]))>0)&&(length(intersect(Candidate_Colorectal,CE$B[i]))>0)){A<-c(A,CE$A[i]);B<-c(B,CE$B[i])}
else if((length(intersect(anchor_colorectal,CE$B[i]))>0)&&(length(intersect(Candidate_Colorectal,CE$A[i]))>0)){A<-c(A,CE$B[i]);B<-c(B,CE$A[i])}
else {}
}
Colorectal_MUeX<-unique(data.frame(A=A,B=B,stringsAsFactors = FALSE))
Colorectal_MutualEx_Candidates<-unique(as.character(Colorectal_MUeX[which(as.character(Colorectal_MUeX[,1])=="KRAS"),2]))
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