Merge branch 'collab'

* collab:
  update hmmBeadStudioSet documentation
  update documentation
  constrain mu for normal state over interval [-.2, .2] rather than [-.1, .1]
  prOutlierBAF is a list with values for initial and max
  contraints on baf outlier probability
  update Rd files for hmmBeadStudioSet and viterbi2Wrapper
  change tolerance default from 1 to 5 in viterbi2Wrapper
  Add unit test for testing the constraints of the BAFs
  constrainMuBaf requires symmetry around the 'AB' mean for the means of AAB and ABB (e.g, 1/3 and 2/3), and symmetry of AAAB and ABBB (e.g, 0.25 and 0.75)
  Fix bug in viterbi2Wrapper where the foreach call to updateBaf passed the entire baf matrix instead of only sample j.
  Ensure forward and backward variables have correct dimension when a matrix is passed to updateBaf
  add function updateBaf
  Estimate mean and variance for BAFs iteratively -- use forward / backward variables from HMM to weight the observations

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@65036 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'collab'

* collab: (72 commits)
  add returnEmission argument to viterbi2Wrapper which is needed by computeBayesFactor in the MinimumDistance package
  The minimum standard deviation for the B allele frequencies is 5e-4.  This avoid Inf values in the emission probability matrix when the updated standard deviation is very small.
  1.19.22: all calls to .getArm include genome build.  Use sampleIds rather than sampleNames(object) to name the GRangesList returned by hmm
  .getArm function loads gap file from SNPchip/inst/extdata, thereby using the genomeBuild info
  Add "[[" method for BafLrrSetList (initializes BafLrrSet)
  Add TroubleShooting section to crlmmDownstream
  remove section header from crlmmDownstream vignette
  crlmmDownstream vignette fits single sample/chromosome before fitting all samples/chromosomes
  add method hmmBeadStudioSetCancer (commented)
  remove trace from unit test
  update crlmmDownstream.  Use constructBafLrrSetListFrom
  update contrainMuBaf
  The outlier probability for log R ratios can be no more than 0.05
  Set BAF means for AA and BB to 0 and 1 respectively
  Add function constructBafLrrSetListFrom
  add function gcPercent
  minor change to viterbiWrapper
  update unit test for oligoSnpSetGT
  Update how the outlier probability is calcualted for copy number.
  Add src/rinit.c
  ...

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@67434 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'collab'

* collab: (32 commits)
  update pdf of vignette
  Add TroubleShooting section to VanillaICE.  Add bset example for chromosome 1.
  check whether diploid state has greater total probability than duplication state.  If so, constrain the duplication state away from the means for the diplid state. (and vice versa)
  If mean for AB genotype not in [.45, .55] set to value in previous update.  If none of the states are estimable, set initial values for diploid cn means at the median value for the chromosal arm
  update default arg for computeLLR
  Add verbose argument to helpfile of viterbi2Wrapper
  Add back rbaf -- called by artificialData function
  Add verbose argument to generatorFun and viterbi2Wrapper
  Export icePlatforms
  update unittests
  remove isAffy from utils.R
  Deleted updateBaf.R
  committing changes to updateBaf.R before deleting
  deleted methods-oligoSnpSet
  Removed methods-matrix.R
  committing methods-matrix before deleting
  move simulation functions in methods-matrix to simulation-functions.R
  relocate fitViterbi.  Remove initialize method for Viterbi2 class and setValidity method. Delete pretty much everything for the Viterbi2 class
  remove the commented hmm2 methods. Comment the setvalidity method for class Viterbi. Move fitViterbi to genotype-functions
  Move hmm functions to file hmm-functions.R
  ...

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@67600 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'collab'

* collab:
  Fix error in unit test that loaded oligoset2 from disk

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@67651 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'collab'

* collab:
  Add [ method for gSetList
  remove fithmm from exports
  IMport as.list from IRanges.  Add "[" method for gRangesList
  add '[[' replacement methods for BafLrrSetList class
  update unit test
  update default minimum for outlier probability of log R ratios
  Constrain lrr outlier probability as min(p, 0.01)
  update stackGRangesList to include column 'sample'
  Fix bug where ... was not passed from hmmBeadStudioSetList to hmmBeadStudioSet
  Reformatting of output for hmmBeadStudioSetList and hmmOligoSetList
  update GRangesList stacking
  stackGRangesList bug fix -- use for loop instead of foreach when number of samples > ocSamples
  Save list object prior to stackGRangesList (for debugging) in hmmBeadStudioSetList

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@69797 bc3139a8-67e5-0310-9ffc-ced21a209358
Bump all packages before creating 2.11 branch.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@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/VanillaICE@70052 bc3139a8-67e5-0310-9ffc-ced21a209358
Estimate starting values for BAF standard deviations.

- Particularly important for Affymetrix
Fix subset method "[" for gSetList class
fix bug in estimation of BAF standard deviation (nonpolymorphic markers were already removed)
Fix bug in hmmBeadStudioSet that occurs when a chromosome arm has fewer than 1000 markers
slight update to droplevels in hmmBeadStudioSet for chromosome arms with few markers