CGHcall: calling aberrations for array CGH tumor profiles.
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.


BACKGROUND
An R-package (GUI), a manual and an example data set are available at http://www.few.vu.nl/~mavdwiel/CGHcall.html.


BACKGROUND
Supplementary data are available at Bioinformatics online.
van de Wiel
Mark A
MA
Department of Pathology, VU University Medical Center, PO Box 7057, 1007MB Amsterdam, The Netherlands. mark.vdwiel@vumc.nl
Kim
Kyung In
KI
Vosse
Sjoerd J
SJ
van Wieringen
Wessel N
WN
Wilting
Saskia M
SM
Ylstra
Bauke
B
D000465:Algorithms; D002869:Chromosome Aberrations; D002874:Chromosome Mapping / Q000379:methods*; D004273:DNA, Neoplasm / Q000235:genetics*; D018628:Gene Dosage / Q000235:genetics*; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
D004273:DNA, Neoplasm