LOHCRP / CRP_LOH v.1
LOHCRP ( or CRP_LOH) is a novel LOH (Loss of heterozygosity) inference and segmentation algorithm based on the conditional random pattern (CRP) model. The new model explicitly considers the distance between two neighboring SNPs, as well as the genotyping error rate and the heterozygous rate. This new method is tested on the simulated and real data of the Affymetrix Human Mapping 500K SNP arrays. The experimental results show that the CRP method outperforms the conventional methods based on the hidden Markov model (HMM).
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Ling-Yun Wu, Xiaobo Zhou, Fuhai Li, Xiaorong Yang, Chung-Che Chang, Stephen T.C. Wong.
Conditional random pattern algorithm for LOH inference and segmentation.
Bioinformatics, Vol. 25, No. 1, 61-67, 2009.