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### release 1.4.0 (23-03-2006) ###
##################################
In daglad:
	- after the "Optimization of Breakpoints" step, clones within the same Level can be splitted if they belong to non-contiguous regions.




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### release 1.3.2 (23-03-2006) ###
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In plotProfile:
	- the user can spefify which varaible used to plot the GNL color code.


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### release 1.3.1 (01-03-2006) ###
##################################
In filterBkp:
	- bug correction when the Normal range is computed (the NormalRef value is correctly taken into account)



##################################
### release 1.3.0              ###
##################################
In glad-function.c
	- bug correction in the GNL affectation when ChekBkpPos is performed


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### release 1.2.0              ###
##################################

same release as 1.1.1 but is was built by bioconductor


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### release 1.1.1 (22-08-2005) ###
##################################

New functions:
	- tkglad: graphical interface for glad function.
	- tkdaglad: graphical interface for daglad function.


In as.profileCGH:
	- LogRatio with infinite values can be set to NA or to some specific value.

##################################
### release 1.1.0 (20-07-2005) ###
##################################

New functions:
	- daglad: new method of array CGH data analysis.
	- roundglad: new function to round numeric data.


In plotProfile:
	- modification to allow abline to be used.


##################################
### release 1.0.4 (18-05-2005) ###
##################################
	- small bug fixed in plotProfile


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### release 1.0.3 (28-04-2005) ###
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In glad function:
	- if there is no breakpoints, no object BkpInfo is returned (otherwise there was error when using plotProfile)


##################################
### release 1.0.2 (21-03-2005) ###
##################################
New functions:
	- as.profileCGH: creation of "profileCGH" object.
	- ChrNumeric: convert chromosome into numeric values.
	- plotProfile: plot genomic profile with breakpoints, outliers, smoothing line and cytogenetic banding.


In arrayPlot function:
	- an option for layout has been added. zlim and bar option have been modified to ensure consistency between them.


In glad function:
	- output contains fields in the same order as the input data plus the specific fields created by glad
	- the outliers MAD are calculated on region with at least a minimal cardinality of msize (msize parameter)
	- there are new attributes for the object profileCGH:

		* SigmaC is a data.frame (with Chromosome and Value fields)
		giving the estimation of the standard deviation for each chromosome
		(based on the Inter Quartile Range estimation).

		* BkpInfo is a data.frame giving the list of breakpoints.

	- lawsglad: you can use smoothfunc="lawsglad" which gives the same results as "laws" bur it runs faster.
	- the parameter mediancenter: if 'TRUE', LogRatio are center on their median. The default behavior in the previous
	GLAD release was to automatically center the LogRatio on their median.
	- The smoothing values correspond to the median of each MSHR (i.e. 'Region'). In the previous release,
	the output of the smoothing function was given.


##################################
### release 1.0.1 (22-10-2004) ###
##################################
Bug fixed in affectationGNL function (the function now works in case of no NA values in the data)

A verbose mode allows to retrieve information on the analysis processing


################################
### release 1.0 (01-04-2004) ###
################################
First version of the GLAD package