## IMPORTANT 
 - move IRanges and oligoClasses back to Suggests? BC moved them to
 Depends just to get rid of annoying warnings while transitioning.
 

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 ### FOR CRLMM
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 - Add RS ids to annotation packages

 - Allele plots
 - M v S plots
 

 R. Scharpf (after next release)
 
 - crlmm should return a SnpSet object with elements A, B, calls, and
   confs in the assayData when save.it=TRUE.  These objects can be very
   big, so...  
 
 - crlmm function should have an option to return nothing and write to
   file a SnpSet object for each chromosome.  This would help the copy
   number part that runs by chromosome

 B Carvalho
 

 - crlmm should return results in CHP files
 

 - crlmm2() with save.it=TRUE must save the original preprocessed intensities
 

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   *                                                         *       
   *                FOR CNRMA                                *
   *                                                         *
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   o Bias adjustment for X chromosome
 
   o Adjust nu for altered copy number (crosshyb)
 
   o Should store parameters in something besides the featureData slot
 
     - Perhaps add a matrix slot for parameters and a slot for batch.
 
     - Need accessors
 
     - how to store parameters for chromosome X (should be nu_A_male,
       nu_A_female, etc.)?
 
   o Provide a SNP- and sample-specific estimate of the variance for
     computing emission probabilities.  (Currently, only SNP-specific)
 
     (DONE -- version 1.3.10

   o Allow a copy-neutral ROH state by not having an equal prior on the
     ellipses.  For instance,

     normal state:  1/4 AA, 1/2 AB, 1/4 BB
     
     copy-neutral ROH:  (1-epsilon)/2 AA,  epsilon AB,  (1-epsilon)/2
     BB

   o Define a class that contains settings for genotyping/copynumber estimation