remove vignettes/VanillaICE.pdf and vignettes/crlmmDownstream.pdf
Fixed bug where log R ratios/copy number were not re-centered.
Merge branch 'collab'

* collab:
  Fixed bug where log R ratios/copy number were not re-centered.
  remove vignettes/VanillaICE.pdf and vignettes/crlmmDownstream.pdf

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@70357 bc3139a8-67e5-0310-9ffc-ced21a209358
INitial estimate of log R ratio variance based on sd.  Do not use zero's when estimating sd of BAF from homozygous genotypes
Require 1 sd separation between deletion and normal state
update sampleNames replacement methods for gSetList (label column names of assayDataList elements)
moved list methods to oligoClasses.  Add function usePennCNVState
No longer imports crlmm. CNSet methods moved to crlmm package
Add methods-GRanges. Includes method for reciprical overlap
update crlmmDownstream vignette
update import from methods package in namespace
@<- has been moved from methods to base, so it no longer needs to
be imported in package NAMESPACEs.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@72298 bc3139a8-67e5-0310-9ffc-ced21a209358
Process all chromosomes at once.  Parallelization:  store ocSamples() of LRRs and BAFs in RAM; use iterators to send columns of LRR and BAF matrix to workers.

Timing:  15 samples using 10 CPUs: 45 minutes / 79G.
Parellization:  pass ff objects to workers.  Workers read from file.
15 samples, ocSamples()=1, 10 workers:  27 minutes, 40G.
add anyNP argument to viterbi2Wrapper
updates to vignette
updates
Add generator-functions.R
update to viterbi2Wrapper.  Handles nupdates=1.  Does not convert to granges when returnEmission is TRUE (not necessary for minimumdistane)
updates to hmm functions