R CGH II: Packages

Start by installing the R packages DNAcopy, aCGH, GLAD and snapCGH.

source("https://bioconductor.org/biocLite.R")
biocLite("DNAcopy")
biocLite("aCGH")
biocLite("GLAD")
biocLite("snapCGH")

For the second part you will need the R package aroma.affymetrix.

In order to use the package devtools you need to make sure you have a working development environment.

• Windows: Install Rtools https://cran.r-project.org/bin/windows/Rtools/.
• Mac: Install Xcode from the Mac App Store.
• Linux: Install a compiler and various development libraries (details vary across different flavors of Linux).

You can install these packages this using:

biocLite("aroma.affymetrix")
install.packages("devtools")
library(devtools)
install_github("HenrikBengtsson/sfit")

---

Next: aCGH

Previous: Intro