Multiple change-point detection via a screening and ranking algorithm

Statistica Sinica

Volumn 23, Issue 4, 2013, Pages 1553-1572

  Hao, Ning ^a   Niu, Yue Selena ^a   Zhang, Heping ^b  

^a University of Arizona   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

Change point detection; Copy number variation; False discovery rate; High dimensional data; Screening and ranking algorithm

Indexed keywords

EID: 84884168489     PISSN: 10170405     EISSN: None     Source Type: Journal    
DOI: 10.5705/ss.2012.018s     Document Type: Conference Paper

References (29)

1. Arias-Castro, E., Donoho, D. L. and Huo, X. (2005). Near-optimal detection of geometric objects by fast multiscale methods. IEEE Trans. Inform. Theory 51.
2. Benjamini, Y. and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57, 289-300.
3. Benjamini, Y. and Yekutieli, D. (2001). The control of the false discovery rate in multiple testing under dependency. Ann. Statist. 29, 1165-1188.
4. Chen, J. and Gupta, A. (2000). Parametric Statistical Change Point Analysis. Birkhauser.
5. Chernoff, H. and Zacks, S. (1964). Estimating the current mean of a normal distribution which is subjected to changes in time. Ann. Math. Statist. 35, 999-1018.
6. Csorgo, M. and Horváth, L. (1997). Limit Theorems in Change-Point Analysis. Wiley, New York.
7. Efron, B. and Zhang, N. R. (2011). False discovery rates and copy number variation. Biometrika 98, 251-271.
8. Gardner, L. A. J. (1969). On detecting changes in the mean of normal variates. Ann. Math. Statist. 40, 116-126.
9. Huang, T., Wu, B., Lizardi, P. and Zhao, H. (2005). Detection of DNA copy number alterations using penalized least squares regression. Bioinformatics 21, 3811-3817.
10. Jeng, X. J., Cai, T. T., and Li, H. (2010). Optimal sparse segment identification with application in copy number variation analysis. J. Amer. Statist. Assoc. 105, 1056-1066.
11. Lai, T. L. and Xing, H. (2011). A simple bayesian approach to multiple change-points. Statist. Sinica 21, 539-569.
12. Lai, T. L., Xing, H., and Zhang, N. (2008). Stochastic segmentation models for array-based comparative genomic hybridization data analysis. Biostatistics 9, 290-307.
13. Nagaev, S. V. (1979). Large deviations of sums of independent random variables. Ann. Probab. 7, 745-789.
14. Niu, S. Y. and Zhang, H. (2012). The screening and ranking algorithm to detect DNA copy number variations. Ann. Appl. Stat. 6, 1306-1326.
15. Olshen, A. B., Venkatraman, E. S., Lucito, R. and Wigler, M. (2004). Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557-572.
16. Page, E. S. (1955). A test for a change in a parameter occurring at an unknown point. Biometrika 42, 523-527.
17. Page, E. S. (1957). On problems in which a change in a parameter occurs at an unknown point. Biometrika 44, 248-252.
18. Peiffer, D. A., Le, J. M., Steemers, F. J., Chang, W., Jenniges, T., Garcia, F., Haden, K., Li, J., Shaw, C. A., Belmont, J., Cheung, S. W. W., Shen, R. M., Barker, D. L. and Gunderson, K. L. (2006). High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res. 16, 1136-1148.
19. Sen, A. and Srivastava, M. S. (1975). On tests for detecting change in mean. Ann. Statist. 3, 98-108.
20. Tibshirani, R. and Wang, P. (2008). Spatial smoothing and hot spot detection for cgh data using the fused lasso. Biostatistics 9, 18-29.
21. van der Vaart, A. and Wellner, J. (1996). Weak Convergence and Empirical Processes. Springer.
22. Vostrikova, L. Y. (1981). Detecting "disorder" in multidimensional random processes. Soviet Mathematics Doklady, 55-59.
23. Wang, K. et al. (2007). PennCNV: An integrated hidden markov model designed for highresolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 17, 1665-1674.
24. Yao, Q. (1993). Tests for change-points with epidemic alternatives. Biometrika 80, 179-191.
25. Yao, Y.-C. (1988). Estimating the number of change-points via Schwarz' criterion. Statistics and Probability Letters 6, 181-189.
26. Yao, Y.-C. and Au, S. T. (1989). Least-squares estimation of a step function. Sankhya A 51, 370-381.
27. Zhang, F., Gu, W., Hurles, M. E. and Lupski, J. R. (2009). Copy number variation in human health, disease, and evolution. Ann. Rev. Genomics and Human Genetics 10, 451-481.
28. Zhang, N. R. (2010). DNA copy number profiling in normal and tumor genomes. Frontiers in Computational and Systems Biology, 259-281.
29. Zhang, N. R. and Siegmund, D. O. (2007). A modified bayes information criterion with applications to the analysis of comparative genomic hybridization data. Biometrics 63, 22-32.