CHANGES IN VERSION 1.7.03 (2012-03-22)

  o fixed missing documentations

CHANGES IN VERSION 1.7.01 (2012-01-16)

  o added remove.duplicates option to pint.match

CHANGES IN VERSION 1.5.35 (2011-10-13)

  o Fixed bugs with GenomeModels accessors

CHANGES IN VERSION 1.5.34 (2011-08-15)

  o changed the default match.probes to TRUE in screen.cgh.mrna; now
    also checks with match.probes = FALSE that the probes are matched

CHANGES IN VERSION 1.5.33 (2011-08-02)

  o now artificially adding arm information if it is missing, to avoid
    halts

CHANGES IN VERSION 1.5.30 (2011-07-15)

  o screen.cgh.mrna option segmented changed into match.probes

CHANGES IN VERSION 1.5.29 (2011-05-09)

BUG FIXES

  o Fixed a bug in plot.ChromosomeModels

CHANGES IN VERSION 1.5.28 (2011-05-09)

BUG FIXES

  o fixed a bug which prevented screeningn while missing values were present

CHANGES IN VERSION 1.5.06 (2011-04-16)

  o added interpretation tools in report.R

CHANGES IN VERSION 1.4.02 (2011-04-16)

  o still correcting critical bug in fixed.window and associated
    functions: now accepting data with no chromosomal arm information

CHANGES IN VERSION 1.4.01 (2011-04-14)

  o corrected critical bug in fixed.window and associated functions

CHANGES IN VERSION 1.3.85 (2011-04-11)

  o Added a method to get the latent variable Z for particular model

CHANGES IN VERSION 1.3.84 (2011-04-10)

  o vignette updated

CHANGES IN VERSION 1.3.83 (2011-04-10)

BUG FIXES

  o Multiple bugs with GenomeModels methods fixed

CHANGES IN VERSION 1.3.82 (2011-04-10)

BUG FIXES

  o plot.ChromosomeArmModels now prints by default the arm in the 
    plot title if only models from one arm is plotted

CHANGES IN VERSION 1.3.80 (2011-03-27)

SIGNIFICANT USER-VISIBLE CHANGES

  o Dependency modeling has been splitted to dmt package.

  o ChromosomeArmModels class is removed from the package.

CHANGES IN VERSION 1.3.71 (2011-03-10)

  o The sign of the effects in z.effects and W.effects now corresponds with the data

CHANGES IN VERSION 1.3.70 (2011-03-04)

BUG FIXES

  o fixed bug which caused an error when using findModel to return a model which is 
    in the end of a chromosome


CHANGES IN VERSION 1.3.69 (2011-03-02)

  o added as.data.frame method

BUG FIXES

  o plot method for GenomeModels now works with showTop argument

CHANGES IN VERSION 1.3.68 (2011-03-02)

  o corrected bibtex bug in doc

CHANGES IN VERSION 1.3.67 (2011-02-01)

  o if row or column names for the data are missing, they are named by
    indices and warning is given (pint.data function)

CHANGES IN VERSION 1.3.66 (2011-01-29)

BUG FIXES

  o pint.data: dimnames now provided for the output data and info fields

CHANGES IN VERSION 1.3.63 (2011-01-13)

BUG FIXES

  o as.data.frame fixed

CHANGES IN VERSION 1.3.63 (2010-01-11)

  o Added many new development features that help to handle segmented
    data (options segmented and nonmatched, and related scripts). Will
    be documented properly in later versions.

CHANGES IN VERSION 1.3.35 (2010-12-30)

BUG FIXES 

  o in pint.match added rownames check between Y$info and
    Y$data, previously only number of rows was checked for Y data. For
    X data things were ok: both row number and row names were checked

  o in pint.data call within pint.match, the X data set was
    erroneously used for both X and Y calls. Now calling Y for Y and X
    for X. Also polishing replace.inf part. Now also naming the info field
    rows correctly.
    
NEW FEATURES
   
  o checking info fields in pint.data for synonymous terms: replacing
    "chromosome" with "chr" and "stop" with "end". Requires less
    tweaking from the end user.

  o if chromosome names X or Y used, replace these with 23 and
    24. This makes code compatible with any organism.

MISC
 
  o changed the internal function name 'impute' to 'imputation'

  o moved some functionality from pint.match to pint.data

CHANGES IN VERSION 1.3.33 (2010-12-09)

BUG FIXES

 o corrected bug in impute.R function which produced NAs

 o added replace.inf in pint.data; now this preprocessing function
   (and consequently pint.match) replaces infinite values with large
   values by default

CHANGES IN VERSION 1.3.32 (2010-12-09)

NEW FEATURES

 o imputation option added (default TRUE) to pint.match and improved
   in pint.data
 

CHANGES IN VERSION 1.3.3 (2010-10-21)

NEW FEATURES

  o GenomeModels and ChromosomeModels classes have getModelNumbers
  method
  o topGenes and topModels methods have default values
  o screen.cgh.mrna checks whether data has been segmented and 
  warns the user

CHANGES IN VERSION 1.3.2 (2010-10-20)

NEW FEATURES

  o Default value for windowSize argument in screening function 
    changed

CHANGES IN VERSION 1.3.1 (2010-10-19)

NEW FEATURES

  o Segmented gene copy number data can be screened with pSimCCA
    method, although it is not recommended.
  o Output type of screening functions can changed to a data frame.
  o All dependency model outputs from screening functions can now
    converted to a data frame with as.data.frame method.
  o ChromosomeArmModels can be accessed with [['p']] and [['q']]
    from ChromosomeModels.

BUG FIXES

  o z.effects gives a proper error message when the window size is
    too large.
  o pCCA method gives a proper error message when the data matrix is not
    invertible.

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