Save a CESAnalysis in progressSource:
Saves a CESAnalysis to a file by calling using base R's saveRDS function. Also updates
run history for reproducibility. Files saved should be reloaded with
Note that the genome reference data associated with a CESAnalysis (refset) is not actually part of the CESAnalysis, so it is not saved here. (Saving this data with the analysis would make file sizes too large.) When you reload the CESAnalysis, you can re-associate the correct reference data.