plotSegmentation: Plot observations and the respective segmentation.

In Vega: An R package for copy number data 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.

Note

If the argument opt=1 then gains and losses are identified by 1 and -1 respectively.

Author(s)

Sandro Morganella, Luigi Cerulo, Giuseppe Viglietto, Michele Ceccarelli Maintainer: Sandro Morganella <[e-mail]>

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)
	

Example output

Processing Chromosome 1
Done

Processing Chromosome 2
Done

Processing Chromosome 3
Done

Processing Chromosome 4
Done

Processing Chromosome 5
Done

Processing Chromosome 6
Done

Processing Chromosome 7
Done

Processing Chromosome 8
Done

Processing Chromosome 9
Done

Processing Chromosome 10
Done

Processing Chromosome 11
Done

Processing Chromosome 12
Done

Processing Chromosome 13
Done

Processing Chromosome 14
Done

Processing Chromosome 15
Done

Processing Chromosome 16
Done

Processing Chromosome 17
Done

Processing Chromosome 18
Done

Processing Chromosome 19
Done

Processing Chromosome 20
Done

Processing Chromosome 21
Done

Processing Chromosome 22
Done

Processing Chromosome X
Done

Processing Chromosome Y
Done

Vega documentation built on April 28, 2020, 8:45 p.m.