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

#####################################
### FOR CRLMM
#####################################
- Add RS ids to annotation packages
- Allele plots
- M v S plots

R. Scharpf 
 
 - harmonize CNSet and FFSet classes
   use-cases:
      - import S3 classes and methods from ff in the NAMESPACE (but this would require installing ff)

      - initialization of FFSet  (can it extend CNSet directly?)
      - subsetting of FFSet objects
      - snp-specific plots  (FFSet or CNSet)
      - batch effect plots  (FFSet or CNSet)
      - with cbs
      - with hmm
 - ff support for Illumina platforms
 - fix all the install warnings
 - add README file to inst/scripts to outline the vignettes
   Vignettes:
      copynumber_SmallData.Rnw    (Affy 5.0 or Affy 6.0.  Fewer than 300 samples)
      copynumber_BigData.Rnw      (Affy 5.0 or Affy 6.0.  300+ samples.  Requires ff package.)
      illumina_copynumber_small.Rnw  (Illumina platforms.  Fewer than 300 samples)
      illumina_copynumber_big.Rnw    (Illumina platforms.  More than 300 samples.  Requires ff package.)
 - documentation for FFSet class/methods
 - bias adjustment for X chromosome
 - where to find examples downstream (smoothing)
 - downstream objects should be similar whether using ff or regular matrices

## this should be moved to vanillaice
## - 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

B Carvalho

- crlmm should return results in CHP files (still can't write CHP files)
- add parallel support (normalization and summarization)