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 3.18.0
Index]