computeFitch_islandGlbSt

This function categorizes CpG islands into methylation states and applies Fitch parsimony
to estimate the minimum number of state changes in a phylogenetic tree.

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

computeFitch_islandGlbSt function

<dl><dt>index_islands</dt>
<dd>A numeric vector specifying the indices of genomic structures corresponding to islands.</dd>
<dt>data</dt>
<dd>A list containing methylation states at tree tips, structured as <code>data[[tip]][[structure]]</code>,
where each tip has the same number of structures, and each structure has the same number of sites across tips.</dd>
<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>u_threshold</dt>
<dd>A numeric threshold value (0-1) defining the unmethylated category.</dd>
<dt>m_threshold</dt>
<dd>A numeric threshold value (0-1) defining the methylated category.</dd>
<dt>testing</dt>
<dd>Logical; if <code>TRUE</code>, returns additional intermediate data.</dd></dl>

Arguments

Compute Fitch Parsimony for Global Methylation States at CpG Islands — computeFitch_islandGlbSt

<dl>

<dt>index_islands</dt>
<dd>A numeric vector specifying the indices of genomic structures corresponding to islands.</dd>


<dt>data</dt>
<dd>A list containing methylation states at tree tips, structured as <code>data[[tip]][[structure]]</code>,
where each tip has the same number of structures, and each structure has the same number of sites across tips.</dd>


<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>u_threshold</dt>
<dd>A numeric threshold value (0-1) defining the unmethylated category.</dd>


<dt>m_threshold</dt>
<dd>A numeric threshold value (0-1) defining the methylated category.</dd>


<dt>testing</dt>
<dd>Logical; if <code>TRUE</code>, returns additional intermediate data.</dd>

</dl>

computeFitch_islandGlbSt: Compute Fitch Parsimony for Global Methylation States at CpG Islands

Description

Usage

Value

Arguments

Details

Examples