VegaMC-package {VegaMC} | R Documentation

## VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer.

### Description

VegaMC enables the detection of driver chromosomal imbalances (deletions, amplifications and loss of heterozygosities (LOHs)) from array comparative genomic hybridization (aCGH) data. VegaMC performs a joint segmentation of aCGH data. Segmented regions are then used into a statistical framework to distinguish between driver and passenger mutations. In this way, significant imbalances can be detected by the associated p-value. VegaMC has been implemented to be easily integrated with the output produced by PennCNV. VegaMC produces in output two web pages allowing a rapid navigation between both detected regions and altered genes. In the web page summarizing the altered genes, the user finds the link to the respective Ensembl gene web page.

### Details

Package: | VegaMC
Type: | Package
Version: | 3.9.3
License: | GPL-2
LazyLoad: | yes

### Examples

        ## Copy the example dataset in current folder
        file.copy(system.file("example/breast_Affy500K.txt", package="VegaMC"),
                                ".")

        ## Analyse data and save results in sorted.txt file
        results <- vegaMC("breast_Affy500K.txt", "results", html=FALSE,
                            getGenes=FALSE)

[Package VegaMC version 3.25.0 Index]