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SWITCHdna is an R library for detection of copy number variation (CNV). The algorithm is based on intensity data from copy number platforms, identifies transition points, and tests the significance using Fisher's exact test, Chi-square approximations, and Wilcoxon rank-sum tests. The library includes a function for visualization of data.


Genetics; DNA; Sequencing; Nucleic acid sites, features and motifs


  • Operation: Copy number estimation
  • Software interface: Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Credit: the NCI Breast SPORE program (P50-CA58223), RO1-CA138255, T32-GM008719, F30-ES018038, R03-CA132143, P50-CA125183, the Breast Cancer Research Foundation, the EIF-Lee Jeans Translational Research Fund, and the V Foundation for Cancer Research.
  • Contact: weigman _at_
  • Collection: -


Weigman VJ, Chao HH, Shabalin AA, He X, Parker JS, Nordgard SH, Grushko T, Huo D, Nwachukwu C, Nobel A, Kristensen VN, Børresen-Dale AL, Olopade OI, Perou CM "Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival." Breast Cancer Res Treat. 2012 Jun;133(3):865-80.
PMID: 22048815
PMCID: PMC3387500

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