1.1.8: Fixed plotGenome so that, when fixVaxes = TRUE horizontal lines are drawn even if there are no points in a certain area. 1.1.7: Removed arguments 'adjust' and 'n' from plotPeaks as it needs to retrieve the same values used in peakPloidy Added option fixVAxes to plotGenome to fix vertical axes to maxRatio and minRatio Fixed plotGenome so that the line from superimpose = "DNACopy" is actually a line and not a series of dots If plotting only one chromosome, instead of plotting chr name, it plots chromosome position. 1.1.6: Added method 'closest' to function peakPloidy for a "standard" normalisation Fixed the 'mode' method Internal tiding 1.1.5: Added methods 'median' and 'mode' to to function peakPloidy for a "standard" normalisation 1.1.4: Fixed an error in exportTable which was providing a meaningless value for SegMean 1.1.3: Changed the provided data (LS041 and CN) to match what bam2windows.pl version 0.3.4 1.1.2: Added an option to plot more colorful genome plots 1.1.1: Corrected a bug in exportTable that crashed if smoothed ratio was not available. 0.1.3.6: Corrected a series of typos in the manual pages and improved the vignette. 0.1.3.5: Added biocViews and specified licence. 0.1.3.4: Added data object CN after peakPloidy is performed.