Merge branch 'collab'

* collab:
  Added neededPkgs() function to use with all %dopar% calls

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MinimumDistance@64689 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'collab'

* collab:
  remove dims method for TrioSet
  Add dims method for TrioSet class
  update plotting functions (xyplotTrio) and vignette
  Bug when looping over the ranges in joint4 if any of the ranges have only one marker.
  Export xyplotTrio (formerly xyplotTrioLrrBaf) and xypanelTrio (formerly xypanelTrioBaf). Add man files for documentation and updated the vignette
  update man file for TrioSet coercion methods
  update dims method for TrioSetList (report number of features)
  narrow function removes splits as a function of the number of mads (previously, removed splits using an absolute value for distance from zero)
  import panel.abline from lattice. Export xyplotTrioLrrBaf and xypanelTrioBaf
  Add replacement method for phenoData for TrioSetList objects
  For computeBayesFactor, remove ranges with sample ids that are not in the TrioSetList object
  use panel.abline to display a grid at -1, 0, log2(3/2) and log2(4/2) in xypanelTrioBaf
  more informative labels for the total log likelihood in joint4 (for internal use)
  Add method to coerce TrioSet to TrioSetList
  update man file for TrioSetList
  Add ffname argument to TrioSetList function.
  bump version
  Add ffprefix argument to TrioSetListLD -- allows user to specify prefix for naming ff objects.
  add ffprefix argument for naming ffobjects when using TrioSetListLD

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MinimumDistance@65035 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'collab'

* collab: (32 commits)
  update MinimumDistance.pdf
  update API with viterbi2Wrapper slightly.  viterbi2Wrapper uses lexical scope for a more efficient HMM implementation / some args changed slightly
  bump version: 1.1.18
  put dataFrameFromRange2 in functions.R
  Update narrow() call in vignette to include featureData
  update xyplotTrio to check for xlim passed through ... operator
  Add genome argument to GenomeAnnotatedDataFrameFromArray method
  Add argument nchar_sampleid to control the number of characters in the sample identifier to display in the panels produced by xyplotTrio. Default is 15.
  update vignette
  Update Rd files
  Do not use stackRangedDataList in computeBayesFactorTrioSetList.  Use do.call("c", object) instead.  stackRangedDataList seems unreliable
  Bug fix in narrow function.  Added genome argument for coersion of RangedData to GRanges
  Update Rd files
  Import fvarLabels
  Add method for coercing RangedDataCNV to GRanges. Update binaries in data/
  Updates for transition to GRanges and genome build annotation
  update dataFrameFromRange2 -- incorrect trio names often displayed in par.strip
  move ingo to author
  Add ingo as maintainer
  parallelize narrow() function.
  ...

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MinimumDistance@67436 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'collab'

* collab:
  Remove emission from package namespace

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MinimumDistance@67650 bc3139a8-67e5-0310-9ffc-ced21a209358
The 'annotation' and 'annotation<-' generics have been moved from Biobase
(2.17.8) to BiocGenerics (0.3.2). All packages that 'setMethods' on these
generics import them from BiocGenerics.



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MinimumDistance@69535 bc3139a8-67e5-0310-9ffc-ced21a209358
merge with bioc trunk

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MinimumDistance@69796 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'collab'

* collab:
  remove checkException calls in unit tests for correct genome annotation
  bump version
  callDenovoSegments in vignette needs to specify genome=hg18

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MinimumDistance@69876 bc3139a8-67e5-0310-9ffc-ced21a209358
comment test for cbs splits
Merge branch 'collab'

* collab:
  comment test for cbs splits

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MinimumDistance@69884 bc3139a8-67e5-0310-9ffc-ced21a209358
Bump all packages before creating 2.11 branch.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MinimumDistance@70050 bc3139a8-67e5-0310-9ffc-ced21a209358
bump package versions after creating 2.11 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MinimumDistance@70052 bc3139a8-67e5-0310-9ffc-ced21a209358