- allow genome to be unset unless using a normalization scheme that actually uses the value of genome.
- retrieve genome from the attribute of the dataset only if it is not explicitly passed in to the morris.normalize function.
- automatically include morrislib.R and profiling.R
- only graph RPS23 for now.
Copy of scatter.R
- eliminate non-coding genes
- eliminate RIKEN genes.
- eliminate genes with a low read count in any dataset
- normalize to Col2a1 expression
- eliminate low read count control experiments
- eliminate all but the most advanced tumor experiments.
Make a histogram of read length from reads around pause site, and from reads outside of pause site.
- first cut at code to find pause sites on genes.  This isn't working yet - it just moves a 9-nucleotide window down the gene calculating the average dept.   I want to try calculating variance and mean for that 9-ht window to see if that is a better decision function to finding pause sites.