            
                RELEASE HISTORY OF HTSCluster PACKAGE
             ========================================


		CHANGES IN HTSCluster VERSION 1.99.0

- Created vignette and doc directories.
- Moved edgeR to IMPORTS rather than DEPENDS.
- Additional plotting option for lambda using ggplot2 and RColorBrewer, both of
  which have been added as dependencies in the namespace.
- Behavior of clusters can now be interpreted with respect to overall gene expression
  (interpretation = "sum" in the PoisMixClus and PoisMixClusWrapper functions) or with
  respect to mean gene expression (interpretation = "mean").
- Added user-specific parameters init.runs (number of small-EM algorithms to
  run for initialization) and init.iter (number of iterations to run within each
  small-EM algorithm).
- Added highDimensionARI function
- Renormalized posterior probabilities after smoothing in probaPost function.
- Removed smoothing option from logLikePoisMix() and implemented numerical
  technique suggested by P. Papastamoulis to calculate log likelihood.
- Mean.filter argument removed from PoisMixClus function.
- Changed "Q" to "UQ" (Upper Quantile), and added "Med" (Median),
  "DESeq" (normalization in DESeq package), and "TMM" (Trimmed Means
  of M values, from the edgeR package) for library size normalization.
- Changed PoisMixClus to estimate a Poisson mixture model for a single
  number of clusters. To estimate a PMM for a series of cluster sizes and
  perform model selection, added the wrapper function PoisMixClusWrapper,
  which enables the user to perform initialization using the small EM strategy
  (as before) or the initialization strategy proposed by Panos Papastamoulis via
  the functions splitEMInit and probaPostInit.
- Added the possibility to estimate model for equally proportioned
  clusters, as well as to include a cluster with fixed parameter values.
- Creation of S3 class "HTSClusterWrapper" and associated S3 methods
  plot.HTSClusterWrapper and summary.HTSClusterWrapper.
- The number of free parameters for the BIC and ICL criteria now does not include
  the n per-gene w parameters, as these are considered to be fixed.

		CHANGES IN HTSCluster VERSION 1.1

- Smoothing option (default = TRUE) has been added to logLikePoisMix() to
  alleviate numerical errors.
- Creation of NAMESPACE, NEWS, and CITATION information.
- Creation of S3 class "HTSCluster" and associated S3 methods plot.HTSCluster
  and summary.HTSCluster. The plot.HTSCluster function now depends on the
  plotrix package, which has been added to Depends in DESCRIPTION.
- Fixed initialization bug for data with non-numerical condition names in
  kmeanInit function.
- License updated to GPL (>=3)

		CHANGES in HTSCLuster VERSION 1.0

This is the first release (7 November 2011).
