An experiment involving two treatment groups compared whole wheat diet and refined wheat diet on different sets of mice. Of interest were the differences by treatment of the levels of hundreds of bacteria in the guts of the mice. It was desired to determine the statistical significance of not only the individual bacteria, but also the families of bacteria. These family relationships are represented in a phylogenetic tree, and it was determined helpful to color the branches of bacteria based on the significance of their corresponding families. Calculating these p-values and coloring the branches by hand would not be a quick process. An automated method would greatly increase the efficiency of these calculations. To handle this problem, SigTree, an R package, was written. The p-values for individual bacteria (tips) are combined up the tree using meta-analysis methods, and significance is visualized on a color scale in a revised phylogenetic tree plot. SigTree is able to handle not only the motivating mouse diet experiment, but also experiments that fall into the general framework of having significance tests (and resulting p-values) on each tip in a phylogenetic tree.
| Identifer | oai:union.ndltd.org:UTAHS/oai:digitalcommons.usu.edu:etd-2316 |
| Date | 01 August 2012 |
| Creators | Jones, Todd R. |
| Publisher | DigitalCommons@USU |
| Source Sets | Utah State University |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | All Graduate Theses and Dissertations |
| Rights | Copyright for this work is held by the author. Transmission or reproduction of materials protected by copyright beyond that allowed by fair use requires the written permission of the copyright owners. Works not in the public domain cannot be commercially exploited without permission of the copyright owner. Responsibility for any use rests exclusively with the user. For more information contact Andrew Wesolek (andrew.wesolek@usu.edu). |
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