coral.stress

Timepoint one is one day of heat-light stress; timepoint two is recovery from it
the next day. Controls are the fragments never exposed to stress. Individual denotes
a coral colony that yielded several fragments for different treatments.

datasets

Quantitative RT-PCR data are analyzed using generalized linear mixed models based on lognormal-Poisson error distribution, fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). The package also implements a lognormal model for higher-abundance data and a "classic" model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. The detailed tutorial is available here: <https://matzlab.weebly.com/uploads/7/6/2/2/76229469/mcmc.qpcr.tutorial.v1.2.4.pdf>.

Mikhail Matz

MCMC.qpcr

Bayesian Analysis of qRT-PCR Data

coral.stress function

A data frame with 64 observations on the following 19 variables.<dl class="dl-horizontal">
 <dt><code>sample</code></dt><dd>a numeric vector</dd>
 <dt><code>individual</code></dt><dd>a factor with levels <code>s1</code> <code>s12</code> <code>s13</code> <code>s15</code> <code>s2</code> <code>s4</code> <code>s5</code> <code>s8</code></dd>
 <dt><code>condition</code></dt><dd>a factor with levels <code>control</code> <code>heat</code></dd>
 <dt><code>timepoint</code></dt><dd>a factor with levels <code>one</code> <code>two</code></dd>
 <dt><code>hsp16</code></dt><dd>a numeric vector</dd>
 <dt><code>actin</code></dt><dd>a numeric vector</dd>
 <dt><code>adk</code></dt><dd>a numeric vector</dd>
 <dt><code>c3</code></dt><dd>a numeric vector</dd>
 <dt><code>chrom</code></dt><dd>a numeric vector</dd>
 <dt><code>clect</code></dt><dd>a numeric vector</dd>
 <dt><code>eif3h</code></dt><dd>a numeric vector</dd>
 <dt><code>g3pdh</code></dt><dd>a numeric vector</dd>
 <dt><code>gsp2</code></dt><dd>a numeric vector</dd>
 <dt><code>hsp60</code></dt><dd>a numeric vector</dd>
 <dt><code>hsp90</code></dt><dd>a numeric vector</dd>
 <dt><code>nd5</code></dt><dd>a numeric vector</dd>
 <dt><code>rpl11</code></dt><dd>a numeric vector</dd>
 <dt><code>spon2</code></dt><dd>a numeric vector</dd>
 <dt><code>ubl3</code></dt><dd>a numeric vector</dd>
 </dl>

Format

RT-qPCR of stress response in coral Porites astreoides — coral.stress

A data frame with 64 observations on the following 19 variables.<dl class='dl-horizontal'>
 <dt><code>sample</code></dt><dd>a numeric vector</dd>
 <dt><code>individual</code></dt><dd>a factor with levels <code>s1</code> <code>s12</code> <code>s13</code> <code>s15</code> <code>s2</code> <code>s4</code> <code>s5</code> <code>s8</code></dd>
 <dt><code>condition</code></dt><dd>a factor with levels <code>control</code> <code>heat</code></dd>
 <dt><code>timepoint</code></dt><dd>a factor with levels <code>one</code> <code>two</code></dd>
 <dt><code>hsp16</code></dt><dd>a numeric vector</dd>
 <dt><code>actin</code></dt><dd>a numeric vector</dd>
 <dt><code>adk</code></dt><dd>a numeric vector</dd>
 <dt><code>c3</code></dt><dd>a numeric vector</dd>
 <dt><code>chrom</code></dt><dd>a numeric vector</dd>
 <dt><code>clect</code></dt><dd>a numeric vector</dd>
 <dt><code>eif3h</code></dt><dd>a numeric vector</dd>
 <dt><code>g3pdh</code></dt><dd>a numeric vector</dd>
 <dt><code>gsp2</code></dt><dd>a numeric vector</dd>
 <dt><code>hsp60</code></dt><dd>a numeric vector</dd>
 <dt><code>hsp90</code></dt><dd>a numeric vector</dd>
 <dt><code>nd5</code></dt><dd>a numeric vector</dd>
 <dt><code>rpl11</code></dt><dd>a numeric vector</dd>
 <dt><code>spon2</code></dt><dd>a numeric vector</dd>
 <dt><code>ubl3</code></dt><dd>a numeric vector</dd>
 </dl>

coral.stress: RT-qPCR of stress response in coral Porites astreoides

Description

Usage

Arguments

Format

Examples