Copy ratio raw and adjusted, table column documentation

[tedtoal]

The segments, genes, and variants output files all contain columns with log2 coverage ratio values in them, unadjusted for purity and ploidy. Here are several suggestions related to this:

1. Make the tables describing output file columns easier to find. Have an entry in the table of contents for them, and perhaps put each one on a separate page. And, make their titles refer to filename arguments to PureCN R program files, not to PureCN functions (which I think you are no longer recommending the user directly call; in fact, the entire document should be changed to reflect the recommended method of using the PureCN programs rather than internal functions).
2. Make sure each time a ratio or copy number column appears, the description says whether or not it is adjusted for purity or ploidy (e.g. log.ratio column in variants file), and whether or not it has been rounded to an integer value. For log ratio, always say log2 in the description.
3. Add a short section to the guide that gives the relationships between raw and adjusted copy number and copy ratio. Use the equations from the paper you referred me to, Zack, Travis I., et al. "Pan-cancer patterns of somatic copy number alteration." Nature genetics 45.10 (2013): 1134, but look into my assertion that his equation for R'(x) is wrong according to his preceding equations.
4. Consider adding additional output file columns containing: (a) raw copy ratio (apply 2^ to log2 ratio); (b) adjusted copy ratio; (c) ploidy; (d) purity (c and d copied from the QC file). If not, just make sure (3) above makes it clear to user what to do to transform the log2 ratio into an adjusted copy ratio.