categorize_siteMethSt

This function categorizes the values in <code>data[[tip]][[structure]]</code> into three categories:<ul>
<li><code>0</code> for unmethylated sites, where values are smaller or equal to <code>u_threshold</code>.</li>
<li><code>0.5</code> for partially methylated sites, where values are between <code>u_threshold</code> and <code>m_threshold</code>.</li>
<li><code>1</code> for methylated sites, where values are larger or equal to <code>m_threshold</code>.</li>
</ul>

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

categorize_siteMethSt function

<dl><dt>data</dt>
<dd>A list structured as <code>data[[tip]][[structure]]</code>, where <code>tip</code> corresponds to tree tips, and <code>structure</code>
corresponds to each genomic structure (e.g., island/non-island).</dd>
<dt>u_threshold</dt>
<dd>A numeric value representing the upper bound for values to be classified as unmethylated (<code>0</code>). Default 0.2.</dd>
<dt>m_threshold</dt>
<dd>A numeric value representing the lower bound for values to be classified as methylated (<code>1</code>). Default 0.8.</dd></dl>

Arguments

Categorize Methylation Frequencies Based on Thresholds — categorize_siteMethSt

<dl>

<dt>data</dt>
<dd>A list structured as <code>data[[tip]][[structure]]</code>, where <code>tip</code> corresponds to tree tips, and <code>structure</code>
corresponds to each genomic structure (e.g., island/non-island).</dd>


<dt>u_threshold</dt>
<dd>A numeric value representing the upper bound for values to be classified as unmethylated (<code>0</code>). Default 0.2.</dd>


<dt>m_threshold</dt>
<dd>A numeric value representing the lower bound for values to be classified as methylated (<code>1</code>). Default 0.8.</dd>

</dl>

categorize_siteMethSt: Categorize Methylation Frequencies Based on Thresholds

Description

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Value

Arguments

Details

Examples