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. Author manuscript; available in PMC: 2009 Jul 15.
Published in final edited form as: Ann Appl Stat. 2008 Jun 1;2(2):687–713. doi: 10.1214/07-AOAS155

Figure 3.

Figure 3

Top: Copy number estimates (vertical axis) versus physical position (horizontal axis) for 9165 SNPs on a simulated chromosome. Bottom: A magnification of regions D, B, and E. High confidence scores for the copy number estimates were simulated for the square points in regions D, B, and E. The two bars beneath the data points in each figure show the predicted hidden states from the vanilla (Van) and ICE HMMs. Note that where the predictions differ in regions D, B, and E, the ICE correctly classified the hidden states. Note that the vanilla HMM also indicates a (spurious) deletion to the left of region A, not indicated by the ICE HMM due to high variability in those copy number estimates.