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    An online copy number variant detection method for short sequencing reads
    (Taylor & Francis Ltd, 2015) Yigiter, Ayten; Chen, Jie; An, Lingling; Danacioglu, Nazan
    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.
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    Group acceptance sampling plans based on time truncated life tests for compound Weibull-exponential distribution
    (Emerald Group Publishing Ltd, 2023) Yigiter, Ayten; Hamurkaroglu, Canan; Danacioglu, Nazan
    Purpose Acceptance sampling plans are a decision-making process on the basis of a randomly selected sampling from a party, where it is not possible to completely scan the products for reasons such as time and cost being limited or the formation of damaged products during the inspection. For some products, the life span (time from beginning to failure) may be an important quality characteristic. In this case, the quality control adequacy of the products can be checked with an acceptance sampling plan based on the truncated life test with a censored scheme for the lifetime of the products. In this study, group acceptance sampling plans (GASPs) based on life tests are studied under the Type-I censored scheme for the compound Weibull-exponential (CWE) distribution. Design/methodology/approach GASPs based on life tests under the Type-I censored scheme for the CWE distribution are developed by using both the producer's risk and the consumer's risk. Findings In this study, optimum sample size, optimum number of groups and acceptance number are obtained under the Type-I censored scheme for the CWE distribution. Real data set illustration is given to show GASPs how to be used for the industry applications. Originality/value Different from acceptance sampling plans with just considering the producer's risk, GASPs are constructed by using two-point approach included both the producer's risk and the consumer's risk for CWE distribution.
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    Poisson, negative binomial, and zero-inflated negative binomial regression models for predicting daily airborne pollen concentration levels in Sinop (Türkiye)
    (Springer, 2025) Yigiter, Ayten; Demir, Cemile Cansi; Hamurkaroglu, Canan; Ozler, Hulya; Kaplan, Ayse; Danacioglu, Nazan; Kaplan, Sumeyra Sezer
    Pollen, produced during the flowering period of plants, especially anemogamous plants that produce high volumes of pollen, poses a risk to individuals with pollen allergies when it is present in the atmosphere. Meteorological factors are known to affect the duration, distribution, and amount of pollen in the air. The remarkable increase in allergic cases in recent years has led to many studies investigating the relationship between pollen and spores that cause allergies and meteorological factors in T & uuml;rkiye as well as in the world. In this study, meteorological factors and their influence on pollen concentrations in the air were examined for the Sinop region in northern T & uuml;rkiye. First, descriptive statistics for pollen obtained from plant taxa were obtained and interpreted. Precipitation, humidity, temperature, and wind speed were considered as meteorological parameters, and the effects of these variables on pollen counts and their annual changes were modelled using Poisson, negative binomial, and zero-inflated negative binomial (ZINB) regression models. The estimation results for all pollen taxa were then discussed. In the models obtained for each pollen type, the statistical significance of the independent variables such as temperature, precipitation, relative humidity, wind speed, time, and lag 1 was found to be different according to the pollen type.