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SIMULATING GENETIC VARIANT DATA FOR
STRUCTURED POPULATIONS USING
AN APPROXIMATE COALESCENT ALGORITHM
by
Hsuan Jung
A Thesis Presented to the
FACULTY OF THE GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
MASTER OF SCIENCE
(BIOSTATISTICS)
May 2007
Copyright 2007 Hsuan Jung
Object Description
| Title | Simulating genetic variant data for structured populations using an approximate coalescent algorithm |
| Author | Jung, Hsuan |
| Author email | hsuanjun@usc.edu |
| Degree | Master of Science |
| Document type | Thesis |
| Degree program | Biostatistics |
| School | Keck School of Medicine |
| Date defended/completed | 2007-03-28 |
| Date submitted | 2007 |
| Restricted until | Unrestricted |
| Date published | 2007-04-24 |
| Advisor (committee chair) |
Marjoram, Paul Stram, Daniel |
| Advisor (committee member) | Conti, David |
| Abstract | In this thesis we develop a program for simulating genetic variants data over long chromosomal region for structured populations. We also implement a simplified version of the algorithm for gene conversion. We show that when recombination, but not gene conversion, is present, the program generates data that is a very close approximation to that generated by the full coalescent model (in terms of LD), given that the migration rate is not too low. The implementation of gene conversion, however, does not yield the same desirable result. However, the program takes less than 2 hours to generate whole chromosomal data, which is impossible given conventional techniques. |
| Keyword | coalescent; simulation |
| Language | English |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Type | texts |
| Legacy record ID | usctheses-m465 |
| Rights | Jung, Hsuan |
| Repository name | Libraries, University of Southern California |
| Repository address | Los Angeles, California |
| Repository email | http://www.usc.edu/isd/libraries/services/ask_a_librarian/email/ |
| Filename | etd-Jung-20070424 |
| Archival file | uscthesesreloadpub_Volume29/etd-Jung-20070424.pdf |
Description
| Title | Page 1 |
| Full text | SIMULATING GENETIC VARIANT DATA FOR STRUCTURED POPULATIONS USING AN APPROXIMATE COALESCENT ALGORITHM by Hsuan Jung A Thesis Presented to the FACULTY OF THE GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Requirements for the Degree MASTER OF SCIENCE (BIOSTATISTICS) May 2007 Copyright 2007 Hsuan Jung |
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