Creating branch for BioC 2.11 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/MinimumDistance@70051 bc3139a8-67e5-0310-9ffc-ced21a209358
Add deprecated function xyplotTrioLrrBaf.  Remove inst/docMinimumDistance.Rnw-- this causes a problem in the R script link on BioC
Add defunct.Rd
Port documentation updates from release branch to devel:

- remove inst/doc/MinimumDistance.Rnw
- add deprecated function xyplotTrioLrrBaf
- document trio states
Improve documentation for computeBayesFactor.Rd
More documentation updates
Merge branch 'collab'

* collab:
  More documentation updates
  Improve documentation for computeBayesFactor.Rd
  Add defunct.Rd
  Add deprecated function xyplotTrioLrrBaf.  Remove inst/docMinimumDistance.Rnw-- this causes a problem in the R script link on BioC
  Creating branch for BioC 2.11 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MinimumDistance@70182 bc3139a8-67e5-0310-9ffc-ced21a209358
v 1.3.3  check for 'seg.means' in values of ranges object for computeBayesFactorTrioSet
Import lrr and baf replacement methods from oligoClassses
change maintainer to RS
Removed Pedigree class definition and corresponding Rd file
Remove class definitions for TrioSet and TrioSetList. Import class definitions from trioClasses
@<- 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/MinimumDistance@72298 bc3139a8-67e5-0310-9ffc-ced21a209358
remove imports from trioClasses
Add MAP, deprecate computeBayesFactor.  Updates compatible with VanillaICE changes
Add generator-funs.  Add back Pedigree Rd files
updates
merge with collab branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MinimumDistance@72706 bc3139a8-67e5-0310-9ffc-ced21a209358