Vega (version 1.20.0)

plotSegmentation: Plot observations and the respective segmentation.

Description

This function allows to plot the observed data superimposing the respective segmentation. By the parameter 'opt' he user can plot the LRR mean values of each segment or the computed aberration kind. In plot window the gain and the loss are identified by a line having value of 1 and -1 respectively.

Usage

plotSegmentation(CNVdata, segmentation, chromosomes, opt = 0)

Arguments

CNVdata

The data matrix.

segmentation

The computed segmentation.

chromosomes

The chromosomes that have to be plotted.

opt

If opt=0 (default) then the LRR mean values are plotted, if opt=1 the computed labels are plotted.

References

Morganella S. et al. (2010). VEGA: Variational segmentation for copy number detection, Bioinformatics.

Examples

	
	# Import the data
	data(G519)
	
	# Compute the segmentation for all chromosomes
	seg <- vega(G519, c(1:22, "X", "Y"))
	
	# Plot the results for all chromosomes in terms of mean of LRRs 
	plotSegmentation(G519, seg, c(1:22, "X", "Y"), opt=0)

	# Plot the results for all chromosomes in terms of aberration kinds
	plotSegmentation(G519, seg, c(1:22, "X", "Y"), opt=1)