R: This function computes, saves and returns the copy number...
vega
R Documentation
This function computes, saves and returns the copy number segmentation on the aCGH data passed as argument.
Description
This function computes the segmentation of the copy number data passed as argument. 'vega' function returns the computed segmentation and save it as a tab delimited file. Users need just to use this function.
This argument is matrix containing the data that have to be analyzed. This matrix must have 4 columns:
- the first row indicates the chromosome;
- the second row indicates the start bp of the probe;
- the third row indicates the end bp of the probe;
- the fourth row reports the measured Log R Ratio;
chromosomes
This is a vector containing the chromosome sthat have to be analyzed. By using c(1:22, "X", "Y") the whole genome will be segmented.
out_file_name
This is the file name used to save the computed segmentation.
beta
This argument is used for the stop condition definition.
min_region_size
This argument specifies the minimum size for the segmented regions.
Value
segmentation
This is a data frame containing the computed segmentation.
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
v <- vega(CNVdata=G519, chromosomes=c(1:22, "X", "Y"), beta=0.5, min_region_size=2);
# Start Vega segmentation on chromosomes 8 of G519 data and save the results in G519_segmentation_chr8.txt tab delimited file
v <- vega(CNVdata=G519, chromosomes=c(8), out_file_name="G519_segmentation_chr8.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.Rd_%03d_medium.png", width=480, height=480)
> ### Name: vega
> ### Title: This function computes, saves and returns the copy number
> ### segmentation on the aCGH data passed as argument.
> ### Aliases: vega
>
> ### ** Examples
>
>
> # Load tha data for Granta-519 Cell Line
> data(G519);
>
> # Start Vega segmentation on all chromosomes of G519 data
> v <- vega(CNVdata=G519, chromosomes=c(1:22, "X", "Y"), 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
>
> # Start Vega segmentation on chromosomes 8 of G519 data and save the results in G519_segmentation_chr8.txt tab delimited file
> v <- vega(CNVdata=G519, chromosomes=c(8), out_file_name="G519_segmentation_chr8.txt", beta=0.5, min_region_size=2);
Processing Chromosome 8
Done
>
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> dev.off()
null device
1
>
providing 
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