Publications by Colleges and Departments (MSU - Bozeman)
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Item Functional Analysis of Variance for Association Studies(Public Library of Science, 2014) Greenwood, Mark C.; Vsevolozhskaya, Olga; Zaykin, Dmitri; Wei, Changshuai; Lu, QingWhile progress has been made in identifying common genetic variants associated with human diseases, for most of common complex diseases, the identified genetic variants only account for a small proportion of heritability. Challenges remain in finding additional unknown genetic variants predisposing to complex diseases. With the advance in next-generation sequencing technologies, sequencing studies have become commonplace in genetic research. The ongoing exome-sequencing and whole-genome-sequencing studies generate a massive amount of sequencing variants and allow researchers to comprehensively investigate their role in human diseases. The discovery of new disease-associated variants can be enhanced by utilizing powerful and computationally efficient statistical methods. In this paper, we propose a functional analysis of variance (FANOVA) method for testing an association of sequence variants in a genomic region with a qualitative trait. The FANOVA has a number of advantages: (1) it tests for a joint effect of gene variants, including both common and rare; (2) it fully utilizes linkage disequilibrium and genetic position information; and (3) allows for either protective or risk-increasing causal variants. Through simulations, we show that FANOVA outperform two popularly used methods – SKAT and a previously proposed method based on functional linear models (FLM), – especially if a sample size of a study is small and/or sequence variants have low to moderate effects. We conduct an empirical study by applying three methods (FANOVA, SKAT and FLM) to sequencing data from Dallas Heart Study. While SKAT and FLM respectively detected ANGPTL 4 and ANGPTL 3 associated with obesity, FANOVA was able to identify both genes associated with obesity.Item Intermediate Statistics with R(2014-01) Greenwood, Mark C.Introductory statistics courses prepare students to think statistically but cover relatively few statistical methods. Building on the basic statistical thinking emphasized in an introductory course, a second course in statistics at the undergraduate level can explore a large number of statistical methods. This text covers more advanced graphical summaries, One-Way ANOVA with pair-wise comparisons, Two-Way ANOVA, Chi-square testing, and simple and multiple linear regression models. Models with interactions are discussed in the Two-Way ANOVA and multiple linear regression setting with categorical explanatory variables. Randomization-based inferences are used to introduce new parametric distributions and to enhance understanding of what evidence against the null hypothesis “looks like”. Throughout, the use of the statistical software R via Rstudio is emphasized with all useful code and data sets provided within the text. This is Version 3.1 of the book.