Estimation of statistical power and false discovery rate of QTL mapping methods through computer simulation

doi:10.1007/s11434-012-5239-3

	Estimation of statistical power and false discovery rate of QTL mapping methods through computer simulation
	Li HuiHui ; Zhang LuYan ; Wang JianKang 1
刊名	CHINESE SCIENCE BULLETIN
	2012
卷号	57 期号:21 页码:2701-2710
关键词	false discovery rate (FDR) inclusive composite interval mapping (ICIM) interval mapping (IM) power simulation
ISSN号	1001-6538
DOI	10.1007/s11434-012-5239-3
通讯作者	Li HuiHui
英文摘要	Many QTL mapping methods have been developed in the past two decades. Statistically, the best method should have a high detection power but a low false discovery rate (FDR). Power and FDR cannot be derived theoretically for most QTL mapping methods, but they can be properly evaluated using computer simulations. In this paper, we used four genetic models (two for independent loci and two for linked loci) to illustrate power and FDR estimation for interval mapping (IM) and inclusive composite interval mapping (ICIM). For each model, we simulated 1000 populations each of 200 doubled haploids. A support interval (SI) was first defined to indicate to which predefined QTL the significant QTL belonged. Power was calculated by counting the number of simulation runs with significant peaks higher than the logarithm of odds (LOD) threshold in the SI. Quantitative trait loci not identified in any SIs were viewed as false positives. The FDR is the rate at which QTLs are identified as significant when they are actually non-significant. Simulation results allowed us to estimate power and FDR of IM and ICIM for two independent and two linkage genetic models. Our estimates allowed us to readily compare the efficiencies of different statistical methods for QTL mapping, including the ability to separate linkage, under a wide range of genetic models. We used IM and ICIM as examples of how to estimate power and FDR, but the principles shown in this paper can be used for power analysis and comparison of any other QTL mapping methods, especially those based on interval tests.
学科主题	Multidisciplinary Sciences ; MULTIDISCIPLINARY SCIENCES
语种	英语
出版者	SCIENCE PRESS
WOS记录号	WOS:000306336100010
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/5147]
专题	作物科学研究所_分子生物学系
作者单位	1.Chinese Acad Agr Sci, Inst Crop Sci, Natl Key Facil Crop Gene Resources & Genet Improv, Beijing 100081, Peoples R China 2.Chinese Acad Agr Sci, CIMMYT China, Beijing 100081, Peoples R China
推荐引用方式 GB/T 7714	Li HuiHui,Zhang LuYan,Wang JianKang. Estimation of statistical power and false discovery rate of QTL mapping methods through computer simulation[J]. CHINESE SCIENCE BULLETIN,2012,57(21):2701-2710.
APA	Li HuiHui,Zhang LuYan,&Wang JianKang.(2012).Estimation of statistical power and false discovery rate of QTL mapping methods through computer simulation.CHINESE SCIENCE BULLETIN,57(21),2701-2710.
MLA	Li HuiHui,et al."Estimation of statistical power and false discovery rate of QTL mapping methods through computer simulation".CHINESE SCIENCE BULLETIN 57.21(2012):2701-2710.