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Bioinformatics. 2007 Apr 1;23(7):892-4. Epub 2007 Jan 31.

CGHcall: calling aberrations for array CGH tumor profiles.

Author information

1
Department of Pathology, VU University Medical Center, PO Box 7057, 1007MB Amsterdam, The Netherlands. mark.vdwiel@vumc.nl

Abstract

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.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
17267432
DOI:
10.1093/bioinformatics/btm030
[Indexed for MEDLINE]
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