Vega (version 1.20.0)

vega: 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.

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.

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);