Yes, once I have them in sets of 12, I use a function in the package Im using (ExomeDepth) to combine all 12 into a GenomicRanges object by parsing the BAM (a binary file type) files. Next, I choose the X I want to test and compare against the other 11. And you’re right in that every file will be an X in a separate round i.e. loop one: file 1 compared to files 2-12, loop two: file 2 against 1,3-12 etc. Comparing them involves running a few functions with the eventual output being a data.frame and a plot. What I’d like to do is write a loop to automate this, including the write.csv part, preferably for all 250 files.

The files are all within a directory, but dispersed in various subdirectories. I’ve created a variable that lists all the files, so my next step is to split that into subgroups of ~12.

I really appreciate your help!