Corrected bug in make.files.for.cpp

Also added ScanTrio.R
Created function CountTU

This function counts the number of transmitted and untransmitted alleles given a table of triostates.
Updated vignettes to do two by two testing.
Added function TU.fish for performing Fisher's exact test with a vector of TU counts
Updated inherited-deletions vignette
Updated inherited-deletion vignette.
Updated inherited-deletion vignette

Added five new figures.
Added function p.min to functions.R

This function finds the minimum component-wise p-value for each region
and returns a DataFrame of regions.  It requires that the GRanges
object in the input DataFrame have name "grange".  An obvious
improvement is to make general both the set function, e.g.,
minimum, and the name of the Granges object, "grange".
Worked on function p.min, but it's still not working correctly yet.
Fixed function p.min.

I seemed to have trouble splitting a DataFrame.  I need to check to
see if the split method is well-defined for DataFrame.
Replace p.min function with f.cmp

f.cmp is a more general function for finding stats by region.  The
arguments are a DataFrame, columname and function.  f.cmp then
performs the function over the set of components in each region. f.cmp
returns a DataFrame.
Added '...' to f.cmp

Now one can pass arguments needed for FUN.
Updated inherited-deletions vignette to use new function f.cmp
Created R markdown version of inherited-deletions vignette
Included html5 version on inherited-deletions vignette
Updated inherited-deletions.Rmd with histogram figure.

I'm having difficulty making a nice table.  I have an html table made via xtable, but it looks crappy and the number of digits is wrong.  In fact it would be better if we could use scientific notation for the p-values.
Merge branch 'collab' of github.com:syounkin/trioClasses into FamilyExperiment
Updated NAMESPACE and AllGenerics after removal of PedClass method.

We now use a PedClass constructor function --- not a method.