Simplify loops

[bschilder]

You can simplify looping over named lists with mapply. This can speed up your code, reduce the number of variables in your namespace (thus conserving memory), and makes it a bit easier to read.

For example:

Before

 ref_in_sample_list <- list()
    # obtain overlapping peaks 
    for(file in peaklist_tidy){
      ref_in_sample <- IRanges::subsetByOverlaps(x = reference_tidy[[1]], 
                                                 ranges = file)
      ref_in_sample_list <- c(ref_in_sample_list, ref_in_sample)
    }
    names(ref_in_sample_list) <- names(peaklist_tidy)

After

  ref_in_sample_list <- mapply(peaklist_tidy, FUN = function(file){
          IRanges::subsetByOverlaps(x = reference_tidy[[1]], 
                                    ranges = file)
      }) 

[serachoi1230]

This was actually in my list of things to do, I'll work on it now! Thank you!!

[bschilder]

I got things started, so let me make my pushes first. Then you can pull down my changes and so what's left to do