Add analysis script

[gadenbuie]

This PR extracts the key elements from the Shiny app into an RScript template. The input values of the app are written into the template before downloading (just the relevant inputs). The script is as self-contained as possible - I used pacman to automatically install missing packages on load and data is downloaded from online sources (including our repo for the HiC contact matrix).

@jhcreed The script does need some attention both to make the variable names more descriptive and to add comments and notes that would be relevant to an end user.

[tgerke]

Nice feature for users wanting to tweak (I wish all Shiny apps I use came with this!); script looks great. I was able to successfully step through it and generate the plot.

• In header section, near "Generated on..." would it be helpful to include the bookmark link for the query as well?
• The as.numeric operations on tad$chr and lad$chr throw warnings (NAs by coercion). Pretty certain these are harmless, but best to anticipate/eliminate if possible
• Agree on better naming descriptions, section commenting, and perhaps even some order reorganizing for clarity (e.g. the plot parameters might most helpfully appear just before the plot is defined, rather than at the top)

[gadenbuie]

@jhcreed This line (and the similar line in in_lad() throw warnings when snp_pos has length > 1 (both in script and app). When length(snp_pos) > 1, I think only the first element is used, so in_tad() only checks the first SNP. You may want to investigate to verify that this is the case or the desired behavior.