main R analysis script

This file contains the main R scripts used to conduct the analysis and produce the figures. It uses as input the "012NA" files (and associated files) produced as described in the "GW_islands_of_diff_processing_scripts.txt" file. Note that two metadata files (also contained in this Dryad package) are also needed. Also crucial is a file of R functions ("genomics_R_functions.R") written especially for this analysis, but designed to work more generally; these functions are called by this script file.