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Development and Application of Tools for Genetic Analysis of Clonal Populations

by Zhian N. Kamvar

Abstract

Research on the population genetics of microbial organisms requires the use of specialized analyses designed for clonal organisms to avoid violating the assumptions of traditional population genetic models. The tools necessary for performing these analyses existed as a set of unrelated software with non-overlapping capabilities and did not cover all aspects of analysis. This meant that researchers not only had to reshape their data into different formats for each analysis, but they also had to switch computing platforms, thus creating a drain in time, and increasing the risk of propagating human error into the analysis. To address this problem, we created the software package poppr, written in the R statistical language, available on all computing platforms. This package is designed for analysis of clonal, partially clonal, and sexual populations, empowering researchers to perform their work in a reproducible manner. We additionally demonstrate the utility of poppr for both plant pathological and theoretical questions by using real-world and simulated data. In chapter 4, we apply these new tools to demonstrate evidence for at least two origins for the outbreak of the Sudden Oak Death pathogen, Phytophthora ramorum in Curry County, Oregon. In chapter 5, we use poppr to assess the power of the index of association with clone-correction, showing that clone-correction has the potential to reduce the power of detecting clonal reproduction. All of the software and analyses in this work were performed in an open and reproducible framework, serving as an example of the power of reproducible research in plant pathology.

Links

Building the document

This was built with the unofficial Oregon State University RMarkdown thesis template. You can find a copy of this template at https://github.com/zkamvar/beaverdown.

This should comply with the thesis guide for Oregon State University. It's based off of the overleaf template

Installation

To install the template, be sure you have the following:

Open RStudio and run the following code:

if (!require("beaverdown")){
  if (!require("devtools") || packageVersion("devtools") < package_version("1.6")){
    install.packages("devtools", repos = "http://cran.rstudio.com")
  }
  devtools::install_github("zkamvar/beaverdown")
}
install.packages("poppr")

Rendering

HTML

Open index.Rmd in RStudio and then hit the "knit" button. Alternatively, you can use:

# In R
bookdown::render_book("index.Rmd")
# In the Terminal
$ ./render.sh
# ----------------------------------------------------------------------
# Rendering HTML
# 
# If you want to render the PDF, set the pdf flag
# 
#     ./render.sh pdf
# ----------------------------------------------------------------------
# 
# 
# 
# processing file: thesis.Rmd
#   |.................................................................| 100%
#    inline R code fragments
# 
# 
# output file: thesis.knit.md
# 
# /usr/local/bin/pandoc +RTS -K512m -RTS thesis.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output thesis.html --smart --email-obfuscation none --standalone --section-divs --table-of-contents --toc-depth 3 --template /Users/zhian/R/bookdown/templates/gitbook.html --number-sections --include-in-header /var/folders/qd/dpdhfsz12wb3c7wz0xdm6dbm0000gn/T//Rtmpyw5Xnp/rmarkdown-strd456e0723e9.html --mathjax --highlight-style pygments --bibliography bib/fronteirs_citations.bib --bibliography bib/main_bibliography.bib --filter /usr/local/bin/pandoc-citeproc
# 
# Output created: _book/1-introduction.html

You can view the rendered html document by typing (in osx):

open _book/1-introduction.html

PDF

# On the command line
./render.sh pdf
# In R, make sure to edit index.Rmd to beaverdown::thesis_pdf
bookdown::render_book("index.Rmd")

You can find the dissertation in _book/dissertation.pdf

Components

_bookdown.yml

This is the main configuration file for the dissertation.

index.Rmd

This file contains all the meta information that goes at the beginning of the pdf document.

pre/

This folder contains all of the Rmd files to be included in the pretext of the dissertation (e.g. abstract, acknowledgments, author contributions, etc.).

There is a slight caveat to all of these files: the very first line must be plain text or the rendering will be screwed up.

chapters/

This folder contains the Rmd files for each chapter in the dissertation.

bib/

This is where any bibliographies may live

csl/

Specific style files for bibliographies should be stored here. A good source for citation styles is https://github.com/citation-style-language/styles#readme

figure/ and data/

These should be self explanatory. Figures and data are stored here.