Rmd refactor (part 7)

[pdiakumis]

Continuation of the general refactor work. Keeping this small-ish for a change.

• reached SV section successfully; need to chat to the curators what exactly they're interested in, since there is a difference with the melted SVs and the way the number of events/variants is calculated. Also adjusted exprTable to handle newer SV object.
• restructured the dev rendering mechanism with params. You now source a file params/sk.R with the params list and that works with both the Run All Chunks Above and an external render.R Rscript. Will demo in our next catchup.
• removed %!in% since was being a pain
• ---Edit: also removed clinical info chunks/data

[pdiakumis]

Merging - I've also removed clinical info chunks/data @skanwal as discussed.