CHANGES IN VERSION 1.1.17 (2010-10-16)

LICENSE

  o Changed license from GPL >=2 to FreeBSD (see
    http://www.freebsd.org/copyright/freebsd-license.html)

DOCUMENTATION

  o Removed netresponse text from vignette IndexEntry (first line). 
    This made netresponse text visible in devel website

CHANGES IN VERSION 1.1.17 (2010-10-15)

HELP & Rd FILE CHANGES

  o sample and genes are displayed in correct order in help pages
    for screening functions

CHANGES IN VERSION 1.1.16 (2010-08-04)

BUG FIXES

  o screening functions can handle chromosomes with fewer samples
  than window size
  o isEmpty method is now exported
  o topModels method for ChromosomeModels class gives no longer
  an error when either arm has no dependency models

CHANGES IN VERSION 1.1.15 (2010-06-16)

SIGNIFICANT USER-VISIBLE CHANGES

  o updates to pint.match function. Now confirms that 'data' and
  'info' fields in the input data matrices are converted to have
  matching elements (corresponding to geneids, for example). Also an
  option to include only selected chromosomes was added. Works now
  with both X/Y or 23/24 annotation for the chromosomes; characters
  and numerics are both ok. Changes affect also the screen.mrna.cgh
  function which calls pint.match (and other functions that call it)

CHANGES IN VERSION 1.1.1 (2010-06-04)

NEW FEATURES

  o matches the samples between cgh and mrna data (screen.cgh.mrna
    function) automatically based on sample names
  o matches genes between cgh and mrna data (screen.cgh.mrna function)
    based on chromosomal locations. User-defined distance threshold
    can be given.

BUG FIXES

  o added robustness towards missing values


CHANGES IN VERSION 0.99.5 (2010-03-28)

SIGNIFICANT USER-VISIBLE CHANGES

  o screen.chromosome function name changed to screen.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