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EagleEye

genome annotation, transcriptome, RNA-seq, ChIP-seq, ChRIP, PARCLIP, cancer, noncoding, long-noncoding RNAS, epigenetics

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RPKM normalization- R script

EagleEye
  • Public
By EagleEye 3188 days ago Comments (1)
P<-read.table("input_table.txt",sep="\t",header=T) len <- ncol(p) rownames(p) <- p[,1] for(i in 2:ncol(p)-1) { d <-p[,i] l <- p[,len] #accessing the length column cS <- sum(as.numeric(p[,i])) #Total mapped reads per sample rpkm[[i]] <- (10^9)*(as.numeric(p[,i]))/(as.numeric(l)*cS) rpkm[[1]] <- p[[1]] } write.table(rpkm,"output_table_rpkm.txt",sep="\t",quote=F,row.names=F)​

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