# # Compare two RNA seq data analysis result files. # # The results files to be compared. file1 = "results1.csv" file2 = "results2.csv" # Read the data files. data1 <- read.csv(file1) data2 <- read.csv(file2) # Select the rows where the FDR is under a cutoff. sig1 <- subset(data1, FDR <= 0.5) sig2 <- subset(data2, FDR <= 0.5) # Extract the gene names only name1 = sig1$name name2 = sig2$name # Intersect: common elements. isect <- intersect(name1, name2) # Elements from both. uni <- union(name1, name2) # Elements in file 1 only. only1 <- setdiff(name1, name2) # Elements in file 2 only. only2 <- setdiff(name2, name1) # Report the differences print("# Tool: compare_results.r") print("") print(paste("# File 1:", length(name1), file1)) print(paste("# File 2:", length(name2), file2)) print("") print(paste("# Union:", length(uni))) print(paste("# Intersect:", length(isect))) print(paste("# File 1 only:", length(only1))) print(paste("# File 2 only:", length(only2))) print("----") print("Only 1:") print(paste( only1)) print("----") print("Only 2:") print(paste( only2)) expect = subset(data1, grepl("UP|DOWN", name))$name