CGHcall: calling aberrations for array CGH tumor profiles
MA Van De Wiel, KI Kim, SJ Vosse… - …, 2007 - academic.oup.com
Bioinformatics, 2007•academic.oup.com
CGHcall achieves high calling accuracy for array CGH data by effective use of breakpoint
information from segmentation and by inclusion of several biological concepts that are
ignored by existing algorithms. The algorithm is validated for simulated and verified real
array CGH data. By incorporating more than three classes, CGHcall improves detection of
single copy gains and amplifications. Moreover, it allows effective inclusion of chromosome
arm information. Availability: An R-package (GUI), a manual and an example data set are …
information from segmentation and by inclusion of several biological concepts that are
ignored by existing algorithms. The algorithm is validated for simulated and verified real
array CGH data. By incorporating more than three classes, CGHcall improves detection of
single copy gains and amplifications. Moreover, it allows effective inclusion of chromosome
arm information. Availability: An R-package (GUI), a manual and an example data set are …
Abstract
Summary: CGHcall achieves high calling accuracy for array CGH data by effective use of breakpoint information from segmentation and by inclusion of several biological concepts that are ignored by existing algorithms. The algorithm is validated for simulated and verified real array CGH data. By incorporating more than three classes, CGHcall improves detection of single copy gains and amplifications. Moreover, it allows effective inclusion of chromosome arm information.
Availability: An R-package (GUI), a manual and an example data set are available at http://www.few.vu.nl/~mavdwiel/CGHcall.html.
Contact: mark.vdwiel@vumc.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
Oxford University Press