compare_CherryFreqs

Performs a chi-squared test to compare the distribution of methylation states
(unmethylated <code>0</code>, partially-methylated <code>0.5</code>, and methylated <code>1</code>)
between two cherry tips. A cherry is a pair of leaf nodes (also called tips or terminal nodes)
in a phylogenetic tree that share a direct common ancestor.

DNA methylation is an epigenetic modification involved in genomic stability,
gene regulation, development and disease.
DNA methylation occurs mainly through the addition of a methyl group to cytosines,
for example to cytosines in a CpG dinucleotide context (CpG stands for a cytosine followed by a guanine).
Tissue-specific methylation patterns lead to genomic regions with different characteristic
methylation levels.
E.g. in vertebrates CpG islands (regions with high CpG content) that are associated to promoter regions of
expressed genes tend to be unmethylated.
'MethEvolSIM' is a model-based simulation software for the generation and modification
of cytosine methylation patterns along a given tree, which can be a genealogy of
cells within an organism, a coalescent tree of DNA sequences sampled from a population, or a species tree.
The simulations are based on an extension of the model of
Grosser & Metzler (2020) <doi:10.1186/s12859-020-3438-5> and allows for changes of
the methylation states at single cytosine positions as well as simultaneous changes of methylation
frequencies in genomic structures like CpG islands.

Sara Castillo Vicente

MethEvolSIM

Simulate DNA Methylation Dynamics on Different Genomic
Structures along Genealogies

Dirk Metzler

compare_CherryFreqs function

<dl><dt>tip1</dt>
<dd>A numeric vector representing methylation states (<code>0</code>, <code>0.5</code>, <code>1</code>) at tip 1.</dd>
<dt>tip2</dt>
<dd>A numeric vector representing methylation states (<code>0</code>, <code>0.5</code>, <code>1</code>) at tip 2.</dd>
<dt>testing</dt>
<dd>Logical; if <code>TRUE</code>, returns additional intermediate data including the contingency table and test result.</dd></dl>

Arguments

Compare Methylation Frequencies Between Two Tips — compare_CherryFreqs

<dl>

<dt>tip1</dt>
<dd>A numeric vector representing methylation states (<code>0</code>, <code>0.5</code>, <code>1</code>) at tip 1.</dd>


<dt>tip2</dt>
<dd>A numeric vector representing methylation states (<code>0</code>, <code>0.5</code>, <code>1</code>) at tip 2.</dd>


<dt>testing</dt>
<dd>Logical; if <code>TRUE</code>, returns additional intermediate data including the contingency table and test result.</dd>

</dl>

compare_CherryFreqs: Compare Methylation Frequencies Between Two Tips

Description

Usage

Value

Arguments

Details

Examples