plotMatrix.R:
	- changed GAGE -> CAGE typo

tried to compile the vignette - did not work
Moved the class definition from readAnnotate.R to genomation-classes.R
genomation-classes.R:
	- changed the order of annotationByGenicParts and
	  annotationByFeature

readAnnotate.R:
	- annotateWithFeature: added intersect.chr
NAMESPACE:
	- added plotGeneAnnotation

readAnnotate.R:
	PlotGenicAnnotation
	- plotGenicAnnotation -> plotGeneAnnotation
	- plotGeneAnnotation works
	- added intersect.chr to annotateWithGeneParts
	- changed the GRangeList.obj variable to feature
readAnnotate.R:
	annotateWithFeatureFlank
	- sorted out chr -> chrs
	- feature -> target in intersect.chr=TRUE
	annotateWithFeature
	- sorted out chr -> chrs
	- feature -> target in intersect.chr=TRUE
readAnnotate.R:
genomation-classes.R:
	- changed annotationByGenicParts -> AnnotationByGeneParts
	- changed annotationByFeature -> AnnotationByFeature
NAMESPACE:
	- randomEnrichment -> RandomEnrichment
	- annotationByFeature -> AnnotationByFeature
	- annotationByGeicParts -> AnnotationByGeneParts

genomation-classes.R:
	- randomEnrichment -> RandomEnrichment

getRandomEnrichment.R:
	- randomEnrichment -> RandomEnrichment
	- getRandomEnrichment returned a list not an object
readAnnotate.R:
	- plotGeneAnnotation now works with cluster=TRUE
readAnnotate.R:
	- annotateWithFeature: feature.name taken by default from
	a variable
readAnnotate.R:
	- sorted the whitespace in the function
readAnnotate.R:
	- show:AnnotationByFeature, made the messages more understandable
Vignette in beta version.