Create GTEXCOEXP.R

petagraph/code/preprocessing/GTEXCOEXP.R

@@ -0,0 +1,22 @@
+#This script needs "GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt" and "GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct"
+#Those files can be otained from "https://gtexportal.org/home/downloads/adult-gtex/metadata" and 
+#"https://gtexportal.org/home/downloads/adult-gtex/bulk_tissue_expression" respectively
+ATR <- read.delim("~/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt", header=FALSE)
+GTX <- read.delim("~/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct", header=FALSE, comment.char="#")
+Genes<-GTX[3:dim(GTX)[1],1:2]
+colnames(GTX)<-GTX[2,]
+GTX<-GTX[3:dim(GTX)[1],3:dim(GTX)[2]]
+GS <- ATR[-1,c(1,7)]
+obsv <- t(t(colnames(GTX)))
+obsv <- obsv[,c(1,1)]
+obsv[,2] <- match(obsv[,1],GS[,1])
+obsv[,2] <- GS[obsv[,2],2]
+Tissues <- t(t(sort(unique(obsv[,2]))))
+for (i in 1:length(Tissues)) {I <- which(obsv[,2]==Tissues[i,1]);D <- GTX[,I];C <- cor(t(D));diag(C)=0;L <- t(t(which(C>=0.99)))}
+l = dim(C)[1];
+L = cbind(L,array("",c(length(L),5)));
+L[,2] = round(ceiling(L[,1]/l));
+L[,3] = L[,1]%%l;L[which(L[,3]==0),3] = l;
+L[,4] = paste("coexpression_",Tissues[i,1],sep = "");
+L[,5] = Genes[L[,2],2];
+L[,6] = Genes[L[,3],2]