A few small changes to inherited deletions vignette.

Cleaned up some whitespace.

Added a line to show the number of regions that are included in analysis.Note that right now regions with one component are not being considered.  It is highly unlikely that a region with over 50 observed deltions will only have one component.  Nonetheless there are a lot of them and we need to consider them.  This will be done soon, but it was a priority to get the figures finished for Terri's progress report.
Fixed bug in new counting method.

This bug was due to the classic R error of expecting a set of indices to have length greater than one.  When there is only one index, the matrix becomes a vector and things fall apart.  It seems to be fixed, but I haven't run it yet on all of the regions.
Update to Inherited Deletions vignette.

No changes since the last commit to the source code.  These changes are just the result of re-running the vignette.  Note that this was a trial and used only the first 100 regions.  Next I need to run it on all of the two thousand some regions.
Having difficulties getting Inherited Deletions vignette running.

Not sure what the problem is here, but I think it might be caching.  Let's see how it goes on my home computer.
Re-ran entire Inherited Deletions vignette.

To be sure that all is well I ran the entire vignette without caching and all is indeed well.  I was worried about some caching issues that may have benn occurring at work.
Updated Inherited Deletions vignette.

Now, we identify the CIs for the two significant regions.  We do so in the CI figures, as well as printing out the values.