Created methods-GWASTools.R

There is one function in this file --- it is not yet a method.  All it does it identify the indices from the snpAnnot GWASTools object.  It is useful for retrieving a subnset of the gebnotype data stored in the ncdf format of GWASTools.
Removed inst from .gitignore
Added allSubjects and intersect2 methods

allSubjects returns all the unique ids in a pedigree object.  Intersect2 is a GRanges method that finds the intersection of all the ranges in a given GRanges object.  I thought this method would exist already, but I couldn't find it.
Removed CNVMatrix* from .gitignore
Merge branch 'FamilyExperiment' of github.com:syounkin/trioClasses into FamilyExperiment

I am not sure what is happening.  sgy
Created trans.tab function

This function computes the p-value for a TDT test using binom.test.
Updated vignettes
Updated vignettes
Added offspring accessor

Also updated .gitignore and deletion-tdt vignette
Created abstract.pdf
Updated deletion-tdt vignette

This is the beginning of the inherited deltion manuscript.  I plan to do it all as a vignette.  I included the bibliography style sheet from BMC as a plaveholder.
Updated deletion-tdt vignette

It now uses BMC article class.
Updated deletion-tdt vignette

Also changed CNVMatrix method a little to return original GRanges object as well.
Fixed a redundnacy in CNVMatrix method
Updated vignettes
Updated vignettes
Updated vignettes
Included results with ScanTrios and updated vignette.
Updated deletion-tdt vignette

Added new figure --- a screen shot from the UCSC genome browser.  Somehow I lost changes to this vignette and I have had to revert to a simpler form.  I don't know why I lost it --- I must have forgot to sync one of my repos?
Updated deletion-tdt vignette

Also included CNVMatrix code for pitt data.