compute_fitch

This function applies Fitch parsimony to determine the minimum number of changes required for
methylation categories at tree tips.

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

compute_fitch function

<dl><dt>tree</dt>
<dd>A rooted binary tree in Newick format (character string) or as an <code>ape</code> phylo object.
Must have at least two tips.</dd>
<dt>meth</dt>
<dd>A matrix of methylation categories at the tree tips, with rows corresponding to tips
(names matching tree tip labels) and columns corresponding to sites or structures.</dd>
<dt>input_control</dt>
<dd>Logical; if <code>TRUE</code>, validates input consistency.</dd></dl>

Arguments

Compute Fitch Parsimony for Methylation Categories — compute_fitch

<dl>

<dt>tree</dt>
<dd>A rooted binary tree in Newick format (character string) or as an <code>ape</code> phylo object.
Must have at least two tips.</dd>


<dt>meth</dt>
<dd>A matrix of methylation categories at the tree tips, with rows corresponding to tips
(names matching tree tip labels) and columns corresponding to sites or structures.</dd>


<dt>input_control</dt>
<dd>Logical; if <code>TRUE</code>, validates input consistency.</dd>

</dl>

compute_fitch: Compute Fitch Parsimony for Methylation Categories

Description

Usage

Value

Arguments

Examples