          CHANGES IN mvGST VERSION 0.99.3 

OTHER CHANGES

	o Removed suppressWarnings() from plot calls of interactiveGraph(),
	  and made arrowheads be 'none' -- to avoid trivial warnings about
	  zero-length arrows of indeterminate angle

	o Cleaned up usage of switch() function calls in graphCell() 
	  and generateGeneSets() functions


          CHANGES IN mvGST VERSION 0.99.2 

BUG FIXES

	o Added section to p.adjust.SFL to have better error catching
      and restrict GO terms to names in rawp (to match Focus Level
	  method)

OTHER CHANGES

	o Added suppressWarnings() to plot calls of interactiveGraph
	  (to avoid trivial warnings about edges that are too short
	  to be plotted, which can happen when the number of GO terms
	  is large in the call to graphCell)

	o Updated nested if/else statements to 'switch' function calls

	o Changed many 'cat' function calls to 'message' or 'warning'

	o Made 'for' loops more robust through use of 'seq_along',
	'seq_len', and 'seq.int'


          CHANGES IN mvGST VERSION 0.99.1 

OTHER CHANGES

	o Modified Description field in DESCRIPTION file
	
	o Reordered import() lines in NAMESPACE file in an attempt
	  to avoid the following two Bioconductor warnings:
        Warning: multiple methods tables found for 'unsplit'
        Warning: replacing previous import by 'IRanges::unsplit' 
		when loading 'GenomeInfoDb'
	  (mvGST does not call 'unsplit' in any way)
	  

	  
	  
          CHANGES IN mvGST VERSION 0.99.0 

OTHER CHANGES

	o Submitted to Bioconductor 8 August 2014


	
	
          CHANGES IN mvGST VERSION 0.1.3 

NEW FEATURES

	o Added package vignette
	
    o Made graphCell more flexible with 'background' colors
	  for graph elements of lesser interest.

    o Made p.adjust.SFL more flexible to control FWER at
	  a user-supplied FWER (rather than automatic 0.05).

    o Implemented minsize and maxsize arguments to restrict
	  sizes of gene sets of interest.

BUG FIXES

	o N/A

OTHER CHANGES

	o N/A
	  

	  
	  
          CHANGES IN mvGST VERSION 0.1.2 

NEW FEATURES

	o Added sample objects in data(mvGSTsamples)	 

BUG FIXES

	o Edited pickOut function to appropriately handle
      non-multivariate profiles (i.e., where results.table
      has only one column, or where only one contrast is of
      interest)	  

OTHER CHANGES

	o Cleaned up package dependencies in DESCRIPTION and
      NAMESPACE files

   	o Cleaned up some .Rd files (especially examples)	 
	  

 
 
          CHANGES IN mvGST VERSION 0.1.1 

NEW FEATURES

  o The default method for accounting for gene name translation 
    issues is now 'method = 2'.

  o The arguments 'contrasts' and 'gene.names' in 'profileTable' 
    are now optional. The information may be passed to 'profileTable'
    as the row and column names of the argument 'pvals'.
  
  o The function 'pickOut' now returns a data frame with the GO 
    descriptions and p-values for each contrasts tested as well as 
    the GO ID.
  
  o The function 'graphCell' now has an optional argument that 
    allows the user to enter the returns from 'pickOut' as the 
    only argument.

BUG FIXES
    
  o The output from 'profileTable' for 1 dimensional profiles 
    now displays correctly.
	
OTHER CHANGES
    
  o Minor clarifications in help files.
  
  o 'pvals' is now the first argument in 'profileTable'.	 
	
