Created PedClass

Created a PedClass class as well as a generator function that takes a data.frame as input.  I am having trouble with instanciating the SNPTrioExperiment object now.  It was working before I changed the class for the pedigree slot to PedClass instead of data.frame.
Created generator function for SNPTrioExperiment

Also updated the geno accessor function to retrieve dim names from row and colData objects.
Updated Vignette
Cleaned up NAMESPACE file and the man pages

moved commented-out text from NAMESPACE to misc/notes either in jhsph directory or gibbons-box home directory
Created trio method and cleaned up PedClass constructor
Updated version in DESCRIPTION
Created GenoTrio method

This method is used to create a list of three SNP matrices corresponding to complete trios
Added reload.R

This file is useful for debugging.  It allows the user to reload the package without having to quit R.
Added reload.R to DESCRIPTIO collate field
Reintroduced Sweave.sty
Added data files to data directory

Also updated the vignette to not rely on outside data.
Updated vignette
Created ctcbind method

Also created functions.R to hold functions not yet converted to methods.
Changed permissions for sample.RData
Created TransCount method

This method will eventually count the number of transmission tat occur within a region specified by a GRanges object.  Ultimately it should work for each range in a Granges object in parallel somehow.
Added '[' method and TransCount method

I'm not sure the TransCount method is working properly.  This is the first step in creating scan-trio.
Updated vignette
Corrected problem with TransCount

There still is a discrepancy with Holger's function.
Fixed ctcbind and added new methods

Added methods include: parents, MAF
Updated '[' methods to include missing i and j
Updated sample data and tried (but failed) to create coercion method