VegaMC-package: VegaMC: A Package Implementing a Variational Piecewise Smooth...

In VegaMC: 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)

VegaMC documentation built on Nov. 8, 2020, 6:48 p.m.