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

This package enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. VegaMC performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, VegaMC produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported.

Author
S. Morganella and M. Ceccarelli
Date of publication
None
Maintainer
Sandro Morganella <morganellaalx@gmail.com>
License
GPL-2
Version
3.12.0

View on Bioconductor

Man pages

sortData
This function sorts a dataset file by the genomic position of...
vegaMC-methods
Class aggregator of VegaMC.
VegaMC-package
VegaMC: A Package Implementing a Variational Piecewise Smooth...

Files in this package

VegaMC/DESCRIPTION
VegaMC/NAMESPACE
VegaMC/R
VegaMC/R/createHTML.R
VegaMC/R/getGenes.R
VegaMC/R/qvalue.R
VegaMC/R/sortData.R
VegaMC/R/vegaMC.R
VegaMC/build
VegaMC/build/vignette.rds
VegaMC/inst
VegaMC/inst/doc
VegaMC/inst/doc/VegaMC.R
VegaMC/inst/doc/VegaMC.Rnw
VegaMC/inst/doc/VegaMC.pdf
VegaMC/inst/example
VegaMC/inst/example/breast_Affy500K.txt
VegaMC/inst/scripts
VegaMC/inst/scripts/sorttable.js
VegaMC/inst/template
VegaMC/inst/template/AberrantGeneTableRow.html
VegaMC/inst/template/AberrantRegionTableRow.html
VegaMC/inst/template/AllRegionTableRow.html
VegaMC/inst/template/Footer.html
VegaMC/inst/template/FooterTable.html
VegaMC/inst/template/HeaderGenes.html
VegaMC/inst/template/HeaderRegions.html
VegaMC/inst/template/HeaderTableAberrantGenes.html
VegaMC/inst/template/HeaderTableAberrantRegions.html
VegaMC/inst/template/HeaderTableAllRegions.html
VegaMC/inst/template/InputParameters.html
VegaMC/inst/template/image
VegaMC/inst/template/image/bioinfologo.png
VegaMC/inst/template/image/ensemblicon.gif
VegaMC/man
VegaMC/man/VegaMC-package.Rd
VegaMC/man/sortData.Rd
VegaMC/man/vegaMC-methods.Rd
VegaMC/src
VegaMC/src/run_vegaMC.c
VegaMC/src/sort_data.c
VegaMC/src/vegaMC.c
VegaMC/vignettes
VegaMC/vignettes/VegaMC.Rnw