CHANGES IN VERSION 0.99.5 (2010-03-28)

SIGNIFICANT USER-VISIBLE CHANGES

  o screen.chromosome function name changed to scree.cgh.mrna
  o methods findHighestGenes and findHighestModels changed to topGenes and topModels 
  o z.projection and W.projection changed to z.effects and W.effects
  o method name 'TPriorpSimCCA' removed and added to 'psimCCA'

NEW FEATURES

  o screening between mirna and cgh added
  o ability to show gene names with highest dependency scores added to plots
  o model can be searched by gene name from output from screen functions
  o model can be calculated around gene by its name
  o order.results methods added which return genes and their dependency scores
  o size of variable name texts can be changed in plot.DependencyModel
  o aliases added to methods (pfa, pcca, pcca.isotropic and ppca)
  o function to format data for packages dependency model calculation added (pint.data)
  o function to pair data sets added (pint.match)

HELP & Rd FILE CHANGES
  o clarified the documentation

DOCUMENTATION
  o model description added to Vignette

CHANGES IN VERSION 0.99.3 (2010-02-23)

SIGNIFICANT USER-VISIBLE CHANGES

  o calculate function name changed to screen.chromosome

NEW FEATURES

  o probabilistic factorial analysis model added
  o argument M in fit.dependency.model changed to H and arbitary matrix
  can be given instead of just identity matrix for pSimCCA method with T prior
  o plot.DependencyModel function added
  o z.projection and W.projection functions added.

HELP & Rd FILE CHANGES

  o changes to examples in help pages

DOCUMENTATION

  o Vignette updatet
  o Collate field added to DESCRIPTION

BUG FIXES

  o all methods of fit.dependency.model are fixed to give full W and phi 
  matrices with correct dimension names

CHANGES IN VERSION 0.99.4 (2010-03-08)

SIGNIFICANT USER-VISIBLE CHANGES

  o default method of screen.chromosome() changed to pSimCCA

NEW FEATURES

  o psimCCA method now accepts data matrices of a different size
  o used method in screen.chromosome() can be determined by parameters only
  o annotation types can be given to plot.DependencyModel() function
  o samples can be ordered in plot.DependencyModel() function according to their
  contribution to dependency model
  o dimension of latent variable z can be given with psimCCA method

BUG FIXES

  o bug fixed that prevented screening the whole genome 
  o show methods now print the used method when only parameters given to screen.chromosome()
  o incorrect gene name in DependencyModel objects corrected