We have developed an R package, snapCGH, for the analysis of array CGH data. It has been written to be compatible with limma so that the user can apply all of the preprocessing functions available within limma to array CGH data.
After the data has been preprocessed and normalised, snapCGH allows the user to apply different segmentation schema available within R using a common style of input object. Additionally, we are developing a wide variety of functions in order to visualise the segmented data and to compare across multiple samples.
The following resources for snapCGH are available:
- practical for reading in and segmenting array CGH data: snapCGH practical I
- data for the first practical: snapCGH practical I data
- practical for comparing and visualising different aCGH segmentation results: snapCGH practical II
- data for the second practical: snapCGH practical II
The latest version of the package can be downloaded from Bioconductor.