An online copy number variant detection method for short sequencing reads

The availability of the next generation sequencing (NGS) technology in today's biomedical research has provided new opportunities in scientific discovery of genetic information. The high-throughput NGS technology, especially DNA-seq, is particularly useful in profiling a genome for the analysis of DNA copy number variants (CNVs). The read count (RC) data resulting from NGS technology are massive and information rich. How to exploit the RC data for accurate CNV detection has become a computational and statistical challenge. We provide a statistical online change point method to help detect CNVs in the sequencing RC data in this paper. This method uses the idea of online searching for change point (or breakpoint) with a Markov chain assumption on the breakpoints loci and an iterative computing process via a Bayesian framework. We illustrate that an online change-point detection method is particularly suitable for identifying CNVs in the RC data. The algorithm is applied to the publicly available NCI-H2347 lung cancer cell line sequencing reads data for locating the breakpoints. Extensive simulation studies have been carried out and results show the good behavior of the proposed algorithm. The algorithm is implemented in R and the codes are available upon request.     

Measures of Association and Visualization of Log Odds Ratio Structure for a Two Way Contingency Table

The odds ratio (OR) is a measure of association used for analysing an I × J contingency table. The total number of ORs to check grows with I and J. Several statistical methods have been developed for summarising them. These methods begin from two different starting points, the I × J contingency table and the two‐way table composed by the ORs. In this paper we focus our attention on the relationship between these methods and point out that, for an exhaustive analysis of association through log ORs, it is necessary to consider all the outcomes of these methods. We also introduce some new methodological and graphical features. In order to illustrate previously used methodologies, we consider a data table of the cross‐classification of the colour of eyes and hair of 5387 children from Scotland. We point out how, through the log OR analysis, it is possible to extract useful information about the association between variables.     

Approximating moments of continuous functions of random variables using Bernstein polynomials

Bernstein polynomials have many interesting properties. In statistics, they were mainly used to estimate density functions and regression relationships. The main objective of this paper is to promote further use of Bernstein polynomials in statistics. This includes (1) providing a high-level approximation of the moments of a continuous function $g\left(X\right)$ of a random variable $X$, and (2) proving Jensen’s inequality concerning a convex function without requiring second differentiability of the function. The approximation in (1) is demonstrated to be quite superior to the delta method, which is used to approximate the variance of $g\left(X\right)$ with the added assumption of differentiability of the function. Two numerical examples are given to illustrate the application of the proposed methodology in (1).     

Monitoring and change-point estimation for spline-modeled non-linear profiles in phase II

In some applications of statistical quality control, quality of a process or a product is best characterized by a functional relationship between a response variable and one or more explanatory variables. This relationship is referred to as a profile. In certain cases, the quality of a process or a product is better described by a non-linear profile which does not follow a specific parametric model. In these circumstances, nonparametric approaches with greater flexibility in modeling the complicated profiles are adopted. In this research, the spline smoothing method is used to model a complicated non-linear profile and the Hotelling T² control chart based on the spline coefficients is used to monitor the process. After receiving an out-of-control signal, a maximum likelihood estimator is employed for change point estimation. The simulation studies, which include both global and local shifts, provide appropriate evaluation of the performance of the proposed estimation and monitoring procedure. The results indicate that the proposed method detects large global shifts while it is very sensitive in detecting local shifts.     

Construction of Simultaneous Confidence Intervals for Ratios of Means of Lognormal Distributions

For constructing simultaneous confidence intervals for ratios of means for lognormal distributions, two approaches using a two-step method of variance estimates recovery are proposed. The first approach proposes fiducial generalized confidence intervals (FGCIs) in the first step followed by the method of variance estimates recovery (MOVER) in the second step (FGCIs–MOVER). The second approach uses MOVER in the first and second steps (MOVER–MOVER). Performance of proposed approaches is compared with simultaneous fiducial generalized confidence intervals (SFGCIs). Monte Carlo simulation is used to evaluate the performance of these approaches in terms of coverage probability, average interval width, and time consumption.     

Suitable Algorithm Associated with a Parameterization for the Three-Parameter Log-Normal Distribution

Associated with a parameterization for the three-parameter lognormal distribution, an algorithm was proposed by Komori and Hirose, which can find a local maximum likelihood (ML) estimate surely if it exists. Nevertheless, by Vera and Díaz-García it was shown that performance in finding a local ML estimate deteriorated by adopting the parameterization only and using other algorithm. In the present article, it will be shown that Komori and Hirose’s algorithm should be used for the parameterization. This work will also give MATLAB codes as a useful tool for the parameter estimation of the distribution.     

情境教学:历史教学的一种有效方法

所谓历史情境教学就是根据情境教学理论、历史学科特点和学生学习历史的认知规律,在历史课的教学过程中,针对具体教学的目的和内容,综合运用多种教学方法和手段,积极创设特定的教学情境。通过在教学实践中遵循情境教学的若干原则和方法,可以激发学生的学习兴趣,进而使学生的主体性得到充分的发挥。     

"处方教学"及其应注意的几个问题

教学方法改革是当前教育改革的重要内容。恰当运用“处方教学”的方法,解决学生在学习中存在的具体问题,成为临床教学改革的一个可供参考的模式。     

论音韵和谐与词语锤炼

古今中外的语言艺术大师都十分重视词语的语言美。我们所说的语言美,主要是指如何使声、韵、调等方面配合协调的问题。现以作家作品的原文和改文为例,运用同义学说来探讨如何从音韵和谐的角度进行词语锤炼的一些基本方法。     

明清小说叙事转换技法谈略——以《金瓶梅》、《红楼梦》为例

明清小说在叙事转换技巧方面已相当成熟,而且理论上也有了相当建树,提出叙事转换须具有简捷性和隐蔽性的要求。同时,在对一些经典小说的评点中,评点家们通过具象性的描述,总结出几种有别于西方叙事理论的一些概念,如"间三带四"、"横云断岭"等。这些概念形象生动,适应了中国读者的审美阅读习惯。它们的运用,打破了传统叙事的单向性和艺术结构的平面化,建构了一个多线发展又浑然一体的立体艺术空间。