#####################################
### FOR CRLMM
#####################################
- 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

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### FOR CNRMA
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- Bias adjustment for X chromosome
- adjust nu for altered copy number (crosshyb)
- a class for the assay data elements and metadata -- oligoSnpSet?
      - should we consider a name change -- e.g., LocusSet
- a class for the intermediate files and methods for SNP-specific plots
- uncertainty estimates for copy number.  Put in cnConfidence slot