A note on statistical method for genotype calling of high-throughput single-nucleotide polymorphism arrays

We study the genotype calling algorithms for the high-throughput single-nucleotide polymorphism (SNP) arrays. Building upon the novel SNP-robust multi-chip average preprocessing approach and the state-of-the-art corrected robust linear model with Mahalanobis distance (CRLMM) approach for genotype calling, we propose a simple modification to better model and combine the information across multiple SNPs with empirical Bayes modeling, which could often significantly improve the genotype calling of CRLMM. Through applications to the HapMap Trio data set and a non-HapMap test set of high quality SNP chips, we illustrate the competitive performance of the proposed method.     

Causality and interdependence analysis in linear econometric models with an application to fertility

This paper is an applied analysis of the causal structure of linear multi-equational econometric models. Its aim is to identify the kind of relationships linking the endogenous variables of the model, distinguishing between causal links and feedback loops. The investigation is first carried out within a deterministic framework and then moves on to show how the results may change inside a more realistic stochastic context. The causal analysis is then specifically applied to a linear simultaneous equation model explaining fertility rates. The analysis is carried out by means of a specific RATS programming code designed to show the specific nature of the relationships within the model.     

Generalized estimating equations for mixtures with varying concentrations

A finite mixture model is considered in which the mixing probabilities vary from observation to observation. A parametric model is assumed for one mixture component distribution, while the others are nonparametric nuisance parameters. Generalized estimating equations (GEE) are proposed for the semi‐parametric estimation. Asymptotic normality of the GEE estimates is demonstrated and the lower bound for their dispersion (asymptotic covariance) matrix is derived. An adaptive technique is developed to derive estimates with nearly optimal small dispersion. An application to the sociological analysis of voting results is discussed. The Canadian Journal of Statistics 41: 217–236; 2013 © 2013 Statistical Society of Canada     

A likelihood ratio test for goodness‐of‐fit of recessive and dominant models for case–control studies

Testing goodness‐of‐fit of commonly used genetic models is of critical importance in many applications including association studies and testing for departure from Hardy–Weinberg equilibrium. Case–control design has become widely used in population genetics and genetic epidemiology, thus it is of interest to develop powerful goodness‐of‐fit tests for genetic models using case–control data. This paper develops a likelihood ratio test (LRT) for testing recessive and dominant models for case–control studies. The LRT statistic has a closed‐form formula with a simple $\chi^{2}(1)$ null asymptotic distribution, thus its implementation is easy even for genome‐wide association studies. Moreover, it has the same power and optimality as when the disease prevalence is known in the population. The Canadian Journal of Statistics 41: 341–352; 2013 © 2013 Statistical Society of Canada     

A Markov regime‐switching model for crude‐oil markets: Comparison of composite likelihood and full likelihood

We use the two‐state Markov regime‐switching model to explain the behaviour of the WTI crude‐oil spot prices from January 1986 to February 2012. We investigated the use of methods based on the composite likelihood and the full likelihood. We found that the composite‐likelihood approach can better capture the general structural changes in world oil prices. The two‐state Markov regime‐switching model based on the composite‐likelihood approach closely depicts the cycles of the two postulated states: fall and rise. These two states persist for on average 8 and 15 months, which matches the observed cycles during the period. According to the fitted model, drops in oil prices are more volatile than rises. We believe that this information can be useful for financial officers working in related areas. The model based on the full‐likelihood approach was less satisfactory. We attribute its failure to the fact that the two‐state Markov regime‐switching model is too rigid and overly simplistic. In comparison, the composite likelihood requires only that the model correctly specifies the joint distribution of two adjacent price changes. Thus, model violations in other areas do not invalidate the results. The Canadian Journal of Statistics 41: 353–367; 2013 © 2013 Statistical Society of Canada     

Fast and Accurate Inference for the Smoothing Parameter in Semiparametric Models

A fast and accurate method of confidence interval construction for the smoothing parameter in penalised spline and partially linear models is proposed. The method is akin to a parametric percentile bootstrap where Monte Carlo simulation is replaced by saddlepoint approximation, and can therefore be viewed as an approximate bootstrap. It is applicable in a quite general setting, requiring only that the underlying estimator be the root of an estimating equation that is a quadratic form in normal random variables. This is the case under a variety of optimality criteria such as those commonly denoted by maximum likelihood (ML), restricted ML (REML), generalized cross validation (GCV) and Akaike's information criteria (AIC). Simulation studies reveal that under the ML and REML criteria, the method delivers a near‐exact performance with computational speeds that are an order of magnitude faster than existing exact methods, and two orders of magnitude faster than a classical bootstrap. Perhaps most importantly, the proposed method also offers a computationally feasible alternative when no known exact or asymptotic methods exist, e.g. GCV and AIC. An application is illustrated by applying the methodology to well‐known fossil data. Giving a range of plausible smoothed values in this instance can help answer questions about the statistical significance of apparent features in the data.     

Forecasting Multivariate Road Traffic Flows Using Bayesian Dynamic Graphical Models,Splines and Other Traffic Variables

Traffic flow data are routinely collected for many networks worldwide. These invariably large data sets can be used as part of a traffic management system, for which good traffic flow forecasting models are crucial. The linear multiregression dynamic model (LMDM) has been shown to be promising for forecasting flows, accommodating multivariate flow time series, while being a computationally simple model to use. While statistical flow forecasting models usually base their forecasts on flow data alone, data for other traffic variables are also routinely collected. This paper shows how cubic splines can be used to incorporate extra variables into the LMDM in order to enhance flow forecasts. Cubic splines are also introduced into the LMDM to parsimoniously accommodate the daily cycle exhibited by traffic flows. The proposed methodology allows the LMDM to provide more accurate forecasts when forecasting flows in a real high‐dimensional traffic data set. The resulting extended LMDM can deal with some important traffic modelling issues not usually considered in flow forecasting models. Additionally, the model can be implemented in a real‐time environment, a crucial requirement for traffic management systems designed to support decisions and actions to alleviate congestion and keep traffic flowing.     

Collapsibility of Conditional Graphical Models

Abstract. In this paper, we consider two kinds of collapsibility, that is, the model‐collapsibility and the estimate‐collapsibility, of conditional graphical models for multidimensional contingency tables. We show that these two definitions are equivalent, and propose a sufficient and necessary condition for them in terms of the interaction graph, which allows the collapsibility to be characterized and judged intuitively and conveniently.     

Testing Monotonicity of Regression Functions – An Empirical Process Approach

We propose several new tests for monotonicity of regression functions based on different empirical processes of residuals and pseudo‐residuals. The residuals are obtained from an unconstrained kernel regression estimator whereas the pseudo‐residuals are obtained from an increasing regression estimator. Here, in particular, we consider a recently developed simple kernel‐based estimator for increasing regression functions based on increasing rearrangements of unconstrained non‐parametric estimators. The test statistics are estimated distance measures between the regression function and its increasing rearrangement. We discuss the asymptotic distributions, consistency and small sample performances of the tests.