vega: This function computes, saves and returns the copy number...

In Vega: An R package for copy number data segmentation

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.

Usage

vega(CNVdata, chromosomes, out_file_name = "", beta = 0.5, min_region_size = 2)

Arguments

CNVdata	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 <[e-mail]>

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);

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