Senior Project Advisor

Anderson, Amy D.

Document Type

Project

Publication Date

Spring 2019

Keywords

Algorithms, Statistics, Alleles, Genotypes, Likelihood, Mathematics

Abstract

In statistical genetics, there are several parameters of a dataset which a researcher might, but which are difficult to estimate in practice. In this paper, we will be focusing on allele frequencies, null alleles, inbreeding coefficients and, to a certain extent, beta values. A common technique for obtaining these values, developed by Amy Anderson and her co-workers, is to jointly estimate all of them using an EM-algorithm and the method of maximum likelihood. Despite this technique being effective in general, it is currently unable to deal with males at X-linked markers. The purpose of this project is to modify the existing algorithm to deal with males at X-linked markers, and conduct simulation testing to see the effect of these unusual markers and identify possible uses. In this paper, we work from the ground up to give readers a basic understanding of the statistics and genetics fundamentals required to grasp the EM-algorithm and subsequent modifications. We also include a discussion of the modifications, as well as the results of our simulations.

Department

Mathematics

Subjects - Topical (LCSH)

Sex-linkage (Genetics)--Mathematical models; Allelomorphism--Mathematical models; Imbreeding--Mathematical models;

Genre/Form

student projects; term papers

Type

Text

Rights

Copying of this document in whole or in part is allowable only for scholarly purposes. It is understood, however, that any copying or publication of this document for commercial purposes, or for financial gain, shall not be allowed without the author’s written permission.

Language

English

Format

application/pdf

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