Add function removeRegionsFoundWithinTransposableElements to remove troughs found within transposable elements in the genome. Create file troughComparisonsWOtransposons.txt which has all valid regions.
Add file tyPositions.txt which has the transposable elements in the yeast genome
Add two functions g4QuadsFoundInRegion and g4QuadsFoundInMultipleRegions which will find all the g4 quadraplexes found in a region given a chromosome and start and end coordinate.
Add files which contain G4 motifs and centromeres in the genome
Add TroughsInClust1WOTransposonsSim.txt and TroughsInClust2WOTransposonsDissim.txt which are files that have troughs in clusters 1 and 2 without those that appear near or within transposons.
Add two files that have troughs in Cluster 1 limited to the number of troughs found in Cluster 2 and these are two randomly sampled trough sets.
Modify this file with lines to calculate p-vals for number of tRNAs found within troughs in Cluster 1 and Cluster 2. Await changes to this file to make it more readable with functions and comments.
Deleted some of the pdfs created from the R script. Not crucial to save in the repo