An R package for copy number data segmentation

Description

Vega (Variational Estimator for Genomic Aberrations) is an algorithm that adapts a very popular variational model (Mumford and Shah) used in image segmentation so that chromosomal aberrant regions can be efficiently detected.

Details

Author(s)

Sandro Morganella, Luigi Cerulo, Giuseppe Viglietto, Michele Ceccarelli Maintainer: Sandro Morganella <morganellaalx@gmail.com>

References

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

Examples

# Load tha data for Granta-519 Cell Line
data(G519);

# Start Vega segmentation on all chromosomes of G519 data and save the results in G519_segmentation.txt tab delimited file
seg <- vega(CNVdata=G519, chromosomes=c(1:22, "X", "Y"), out_file_name="G519_segmentation.txt", beta=0.5, min_region_size=2);

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Vega)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Vega/Vega-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Vega-package
> ### Title: An R package for copy number data segmentation
> ### Aliases: Vega-package Vega
> 
> ### ** Examples
> 
> 
> # Load tha data for Granta-519 Cell Line
> data(G519);
> 
> # Start Vega segmentation on all chromosomes of G519 data and save the results in G519_segmentation.txt tab delimited file
> seg <- vega(CNVdata=G519, chromosomes=c(1:22, "X", "Y"), out_file_name="G519_segmentation.txt", beta=0.5, min_region_size=2);
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

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>