0.0.2 added functions.R
0.0.5 changed SaveImage to LazyLoad
0.0.6 change \VignetteIndexEntry in the vignette
0.0.7 added Statistics to BiocViews.  Slight change to vignette.
0.0.8 fixed subsetting of emission probabilities in HmmSnpSet
0.0.9
	-added support for confidence estimates for the 500k platform (250k Nsp and 250k Sty)
	
	-updated help pages for hmm, hapmapProbabilities,
	getHapmapProbabilities, getCallEmission
	
	-updated callEmission to check for 'enzyme' in featureData and to
	check that the annotation is one of the packages that we support

	- added an example for callEmission
	
	- added a check for the callsConfidence package if the ICE option
	is selected for the hmm

0.1.0  **Migrating to allow fitting the HMM to multiple samples/multiple chromosomes **

	- removed the slot predictions from the class definition of HmmSnpSet
	- Made predictions an element of the AssayData
	- predictions is a matrix
	
	- changed the "[" method for the HmmSets to subset the prediction
	matrix appropriately

	- emissionProbability and likelihood slots are matrices for one
	experiment.  would have to store this as a list.  Probably best to
	not store this information by default.  And only keep the matrix
	when debugging a single sample.  Changed the class of
	emissionProbability and likelihood to 'NullOrMatrix' and the
	initial default to NULL.  Similarly, the default is not to keep
	the transition probabilities.

	- added arguments keepEmission, keepLikelihood, and
	keepTransitionProb (all set to FALSE) to the hmm method

	- rewrote the hmm method to run on all samples.  So for each non-X
	chromosome, the hmm is run for all samples in the object.
	
	- changed default of sample argument in method hmm from NULL to
	1:ncol(object) (by default, hmm runs on all samples)

	- hmm no longer subsets when genotype values are missing, though
	it will only run on the complete genotypes.  Where genotypes are
	missing, the prediction will be NA.  **Could be improved**

	- added argument for sample to getCopyNumberScale (default is first sample)
	- added replacement method for "["
	- removed scaleCopyNumber and locationCopyNumber from class definition of HmmSnpCallSet
	- added  breakpoint methods
	
	- Removed the chr1 data example.  Replaced this example with
	chromosome1 -- this example includes the predictions from the ICE
	HMM

	- the vignette now includes a comparison of the vanilla and ICE
	HMMs fit to the simulated data in the chromosome1 example

        - removed missing values in getCopyNumberScale
	- check whether location of copy number is NULL before assigning default values

	- because Illumina intensities are ratios, I added a check for
	is.nan and removed these values

	- check for is.nan in plotHmm method
	- added argument at to plotHmm for the y-coordinates

0.1.1   
	- getCopyNumberLocation checks annotation slot.  If annotation is
	Illumina500k, the hidden states are ratios.
	- hmm method sets log2 slot to FALSE if annotation is Illumina500k

	- default argument for arm is "both" for both hmmWrapper and hmm

        - defined superclass hSet for HmmSnpSet, HmmSnpCallSet, and HmmSnpCopyNumberSet
	- rewrote hmm to work for multiple samples/multiple chromosomes.  returns a list.
	We now fit the hmm chromosome by chromosome to all samples in the object.
	- method breakpoints returns physical positions (start and stop) of altered states

	- fixed bug in plotHmm 

	- allow different probabilities for a homozygous call for deletion
	and copy neutral regions.  This would fix the potential problem of
	not identifying a deletion since CRLMM can make heterozygous
	genotype calls in regions where the copy number is not 2

	- changed the class definitions of HmmSnpCallSet and HmmSnpSet by
	having a slot for pCHOM.  This is the probability of a homozygous
	genotype call conditional on the hidden state.  The ordering
	should be the same as the ordering of hidden states.

	- hmm is working for all three classes

	- updated vignette to show an example of the hmm for each of the
	three classes

	- added a method plotBreaks that allows close up views for each of
	the altered regions detected by the HMM -- by default, this is
	interactive

0.1.2   Fixed bug in plotBreaks
	ad-hoc parameter for reducing number of LOH hits
	Fit to each chromosomal arm when "both" is selected
	breakpoints defined for hSet
	added col.centromere and legend arguments to plotHmm

0.1.3   added previous_SNP and next_SNP to .break()
	added checks in breakspoints() to prevent an error when there are no breaks
	removed callsConfidence from suggests and require() statements from functions.R, methods-HmmSnpCallSet, methods-HmmSnpCopyNumberSet

0.1.4   replaced instances of \code{"\linkS4class{}"} with \code{\linkS4class{classname}} or \code{link{classname-class}}
	rewrote vignette so that texi2dvi("ICE.tex", pdf=TRUE, clean=FALSE, quiet=FALSE) works without error

0.1.5	fixed bug in calculating centromere coordinates
	Depends on R-2.6.0
	
	removed "method" from class definitions and methods.  Added
	callsIce and copyNumberIce to class definitions and methods

	added cytobands by default for plotHmm

	Depends on SNPchip >= 1.1.14 and R-2.6.0 

0.1.6   
	Depends on SNPchip >= 1.1.15:  Note that this means that ICE no
	longer depends on oligo

	Removed plots from vignette

0.1.7  
	changes to visualization functions: plotBreaks and plotHmm
	added function locateCytoband
	breakpoints now included cytobands for non-normal hidden states and information 
	   about the proportion of heterozygous genotype calls, etc.
	plotHmm adds the cytoband location above the prediction bar
	plotBreaks method for list()
	remove cytoband plots from vignette
	fixed helpfile links 

0.1.9  	Changed name to VanillaICE

0.1.11  Changed class definitions:
	- hSet extends SnpLevelSet (not oligoSnpSet)
	- HmmSnpSet extends hSet (not HmmSnpCopyNumberSet and HmmSnpCallSet)
	
	
 	
Next release:  

	**getCallEmission should extract confidence scores from callsConfidence
	AssayDataElement if the genotype calls were processed by CRLMM -
	add a check to see if genotype calls were processed by crlmm.  -

	- add a summary method (maybe based on breakpoints output?)
	- write a function that calculates empirical estimates for HMM parameters

	Add SCALE or transitionScale ... to class definition of hSet

	add more options for par and plotCytoband in plotHmm (height, mar, oma)

	add options for plotCytoband in plotBreaks

	rewrite plotHmm, plotBreaks, etc. 
           -- define a core method for hSet and use callNextMethod(extensively)


