Changed SNPTrioExperiment to FamilyExperiment

Also removed CNVTrioExperiment
Created CNVMatrix method and started deletion-tdt vignette

Also removed CNVTrioExperiment vignette.
Tidied up a bit

I removed setdiff since it is no longer being used, and I renamed 'relist.sgy' 'TrivialGRangesList'
Updated DESCRIPTION
TrioAssay, cnv(), and reduce() in CNVMatrix()

Added the accessor method cnv() and renamed GenoTrio to TrioAssay.

CNVMatrix() was giving counts greater than one indicating that the subject overlapped with themselves because the component GRanges object is a non-overlapping partition.  Thus if anything were to overlap it would be between subjects, and in CNVMatrix we do one subject at a time.  So, there is a problem with self-overlap in the PennCNV data, which likely will lead to overcounts, and therefore false positives.
Cleaned up unit test files

Also removed an empty example from the trioClasses man page.
Added type argument to TrioAssay call
Fixed bug in geno branch of TrioAssay

I changed it back to coercion to numeric matrix (0,1,2) from SnpMatrix.
Updated deletion-tdt vignette
Updated vignette trioClasses
Added Rprof file and updated trioClasses vignette