Updated CNVMatrix.pdf
Updated deletion-tdt vignette
Updated trioClasses vignette
Merge branch 'FamilyExperiment' of github.com:syounkin/trioClasses into FamilyExperiment
Updated trioClasses vignette
Updated trioClasses vignette
Updated trioClasses vignette
Updated trioClasses vignette
Updated trioClasses vignette
Updated CNVMatrix() to accept/require a second granges object to be used for comparison.  In the case of the deletion TDT we use the control granges object so that we may directly compare.  It may be better to have the argument be the scaffold and not the controls.  The scaffold is disjoin(cses,controls).
Updated CNVMatrix vignette.
Updated CNVMatrix() to use disjoin() properly, and updated CNVMatrix vignette accordingly.
Updated version number in DESCRIPTION.
Created inherited-deletions vignette

This vignette will contain results for varying values of coverage threshold as well as a common scaffolding for the CNV components between cases and controls.
Updated deletion-tdt vignette
Updated CNVMatrix vignette
Included window object in output of ScanTrio()
Merge branch 'FamilyExperiment' of github.com:syounkin/trioClasses into FamilyExperiment

Made a change to ScanTrio() while working branch was not up to date.
Merge branch 'Scaffold' of github.com:syounkin/trioClasses into Scaffold

Just trying to have a local Scaffold branch on jhsph-box.  I think I must niot be doing this the best way.
Now computes log(lr) when p.in > q.in and returns log(lr)=0 when not