A new Bayesian approach for QTL mapping of family data

Author(s):  
Daiane Aparecida Zuanetti ◽  
Luis Aparecido Milan

In this paper, we propose a new Bayesian approach for QTL mapping of family data. The main purpose is to model a phenotype as a function of QTLs’ effects. The model considers the detailed familiar dependence and it does not rely on random effects. It combines the probability for Mendelian inheritance of parents’ genotype and the correlation between flanking markers and QTLs. This is an advance when compared with models which use only Mendelian segregation or only the correlation between markers and QTLs to estimate transmission probabilities. We use the Bayesian approach to estimate the number of QTLs, their location and the additive and dominance effects. We compare the performance of the proposed method with variance component and LASSO models using simulated and GAW17 data sets. Under tested conditions, the proposed method outperforms other methods in aspects such as estimating the number of QTLs, the accuracy of the QTLs’ position and the estimate of their effects. The results of the application of the proposed method to data sets exceeded all of our expectations.

Data Mining ◽  
2011 ◽  
pp. 1-26 ◽  
Author(s):  
Stefan Arnborg

This chapter reviews the fundamentals of inference, and gives a motivation for Bayesian analysis. The method is illustrated with dependency tests in data sets with categorical data variables, and the Dirichlet prior distributions. Principles and problems for deriving causality conclusions are reviewed, and illustrated with Simpson’s paradox. The selection of decomposable and directed graphical models illustrates the Bayesian approach. Bayesian and EM classification is shortly described. The material is illustrated on two cases, one in personalization of media distribution, one in schizophrenia research. These cases are illustrations of how to approach problem types that exist in many other application areas.


Author(s):  
M. Azarkhail ◽  
M. Modarres

The physics-of-failure (POF) modeling approach is a proven and powerful method to predict the reliability of mechanical components and systems. Most of POF models have been originally developed based upon empirical data from a wide range of applications (e.g. fracture mechanics approach to the fatigue life). Available curve fitting methods such as least square for example, calculate the best estimate of parameters by minimizing the distance function. Such point estimate approaches, basically overlook the other possibilities for the parameters and fail to incorporate the real uncertainty of empirical data into the process. The other important issue with traditional methods is when new data points become available. In such conditions, the best estimate methods need to be recalculated using the new and old data sets all together. But the original data sets, used to develop POF models may be no longer available to be combined with new data in a point estimate framework. In this research, for efficient uncertainty management in POF models, a powerful Bayesian framework is proposed. Bayesian approach provides many practical features such as a fair coverage of uncertainty and the updating concept that provide a powerful means for knowledge management, meaning that the Bayesian models allow the available information to be stored in a probability density format over the model parameters. These distributions may be considered as prior to be updated in the light of new data when they become available. At the first part of this article a brief review of classical and probabilistic approach to regression is presented. In this part the accuracy of traditional normal distribution assumption for error is examined and a new flexible likelihood function is proposed. The Bayesian approach to regression and its bonds with classical and probabilistic methods are explained next. In Bayesian section we shall discuss how the likelihood functions introduced in probabilistic approach, can be combined with prior information using the conditional probability concept. In order to highlight the advantages, the Bayesian approach is further clarified with case studies in which the result of calculation is compared with other traditional methods such as least square and maximum likelihood estimation (MLE) method. In this research, the mathematical complexity of Bayesian inference equations was overcome utilizing Markov Chain Monte Carlo simulation technique.


2001 ◽  
Vol 58 (8) ◽  
pp. 1663-1671 ◽  
Author(s):  
Milo D Adkison ◽  
Zhenming Su

In this simulation study, we compared the performance of a hierarchical Bayesian approach for estimating salmon escapement from count data with that of separate maximum likelihood estimation of each year's escapement. We simulated several contrasting counting schedules resulting in data sets that differed in information content. In particular, we were interested in the ability of the Bayesian approach to estimate escapement and timing in years where few or no counts are made after the peak of escapement. We found that the Bayesian hierarchical approach was much better able to estimate escapement and escapement timing in these situations. Separate estimates for such years could be wildly inaccurate. However, even a single postpeak count could dramatically improve the estimability of escapement parameters.


2021 ◽  
Vol 14 (2) ◽  
pp. 231-232
Author(s):  
Adnan Kastrati ◽  
Alexander Hapfelmeier

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