
Changes in version 1.99.4:

SIGNIFICANT USER-VISIBLE CHANGES
  
    o Typos in the vignette are fixed.
	
Changes in version 1.99.3:

BUG FIXES

    o mosaicsFit(): mismatch between function and help fixed.
	
	
Changes in version 1.99.2:

SIGNIFICANT USER-VISIBLE CHANGES
  
    o mosaicsFit(): Sets bgEst="rMOM" as default.

    o Help documents are polished and updated.

    o Vignette is updated.
	
	
Changes in version 1.99.1:

SIGNIFICANT USER-VISIBLE CHANGES

    o mosaicsFitHMM() & mosaicsPeakHMM(): Hidden-Markov-Model-based MOSAiCS model fitting & peak calling, respectively, to identify broad peaks such as histone modifications.
	
    o Add new class 'MosaicsHMM' with methods show(), plot(), & estimates().
	
    o mosaicsFit(): Introduces a new argument 'trans'.
	
    o mosaicsFit(): Stability & robustness of model fitting were improved.

    o Polish help documents of constructBins(), generateWig(), and mosaicsRunAll().
	
    o Tested to work with >= R 3.0 properly.

BUG FIXES

    o constructBins() & export(): Use correct base for BED file (one base shift).
	
    o Reflect the changes in Rcpp packages that mosaics package depends on.
    
	
Changes in version 1.5.3:

BUG FIXES

    o mosaicsRunAll(): Bug fix when byChr = TRUE.


Changes in version 1.5.2:

SIGNIFICANT USER-VISIBLE CHANGES

    o constructBins(): Supports aligned read file formats for PET data (eland results and SAM formats). 

    o mosaicsRunAll(): Supports aligned read file formats for PET data. 
    
    o Add generateWig(): Constructs wiggle files for PET and SET data. 
    
    o Use tab separator instead of whitespaces for generateWig() and constructBins().
    
    o Improve the vignette (case studies, example lines for input files, generateWig()).

BUG FIXES

    o constructBins(): Bug fix for capping and excludeChr. Fix incorrect summary when byChr = TRUE.

    o mosaicsRunAll(): Bug fix for excludeChr & handling the full path for chipFile and controlFile.


Changes in version 1.5.1:

SIGNIFICANT USER-VISIBLE CHANGES

    o constructBins(): Chromosome information can now be specified. 
    
    o mosaicsRunAll(): Chromosome information can now be specified. 


Changes in version 1.4.1:

BUG FIXES

    o constructBins(): Bug fix for the "outfileLoc" argument. 

    o mosaicsFit(): Minor changes in two-signal-component model fitting.

    o mosaicsPeak(): No warning with the updated IRanges package.
    
	
Changes in version 1.4.0:

   o BioConductor release 2.10.


Changes in version 1.3.4:

SIGNIFICANT USER-VISIBLE CHANGES

    o Improve help documents for all classes and functions.
    
BUG FIXES

    o mosaicsPeak(): Correct bin size calculation when binsize=NA.
    
Changes in version 1.3.2:

SIGNIFICANT USER-VISIBLE CHANGES

    o Simplify arguments of mosaicsRunAll(), constructBind(), and export().
    
    o Add parallel argument in mosaicsFit().

    o Extensive use of parallel processing/computing.

    o Overall speed improvements in the package.
    
    o Update the vignette.
    
    o Use parallel package instead of multicore package.
    
Changes in version 1.2.5:

    o Correct version number in DESCRIPTION and package?mosaics.

Changes in version 1.2.4:

SIGNIFICANT USER-VISIBLE CHANGES
    
    o Add parallel argument in readBins().
    
    o Add parallel argument in mosaicsRunAll().

BUG FIXES

    o DESCRIPTION: 'multicore' package in 'Enhances' instead of 'Suggests'.

Changes in version 1.2.3:

NEW FEATURES

    o New model for deeply sequenced ChIP-seq data.
    
    o Genome-wide analysis of ChIP-seq data is now available.
    
    o Supports more aligned read file formats: eland_result, eland_extended, eland_export, bowtie, SAM, BED, CSEM.
    
    o Preprocessing of aligned read files can be done within the R environment using constructBins().
    
    o Easier model fitting for the two sample analysis using mosaicsRunAll().
    
    o Preprocessing and model fitting become much faster (Rcpp).
    
    o Parallel processing/computing is now supported (multicore).

SIGNIFICANT USER-VISIBLE CHANGES
    
    o Add constructBins(): Preprocess aligned read files to bin-level files.
    
    o Add mosaicsRunAll(): Convenient two sample analysis.
    
    o Add bgEst argument in mosaicsFit(): Choose background estimation approach.
    
    o Add nCore argument in readBins(): Parallel processing.
    
    o Vignettes is now extensively updated.
    
    o Rcpp package is required and multicore package is suggested.

DEPRECATED AND DEFUNCT

    o Drop chrID argument in export().

BUG FIXES

    o Fix mosaicsPeak() for the case that no peak is called.
    
    o Fix export() by removing unnecessary spaces in output text files.
    
Changes in version 1.2.0:

   o BioConductor release 2.9.
   
Changes in version 1.0.1:

   o Fixes for 'plot' method of class 'binData'.
   
Changes in version 1.0.0:

   o On BioConductor (release 2.8).
