validate_structureIndices

This function checks whether the provided indices for islands and non-islands
are within the valid range of structures in the dataset. It also warns if
any indices are present in both <code>index_islands</code> and <code>index_nonislands</code>.

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

validate_structureIndices function

<dl><dt>data</dt>
<dd>A nested list <code>data[[tip]][[structure]]</code>.
Assumes that the number of structures is consistent across tips and that
within each structure, all tips have the same number of sites.
The number of structures is inferred from <code>length(data[[1]])</code>.</dd>
<dt>index_islands</dt>
<dd>An integer vector specifying indices that correspond to island structures.</dd>
<dt>index_nonislands</dt>
<dd>An integer vector specifying indices that correspond to non-island structures.</dd></dl>

Arguments

Validate Structure Indices for Island and Non-Island Data — validate_structureIndices

<dl>

<dt>data</dt>
<dd>A nested list <code>data[[tip]][[structure]]</code>.
Assumes that the number of structures is consistent across tips and that
within each structure, all tips have the same number of sites.
The number of structures is inferred from <code>length(data[[1]])</code>.</dd>


<dt>index_islands</dt>
<dd>An integer vector specifying indices that correspond to island structures.</dd>


<dt>index_nonislands</dt>
<dd>An integer vector specifying indices that correspond to non-island structures.</dd>

</dl>

validate_structureIndices: Validate Structure Indices for Island and Non-Island Data

Description

Usage

Value

Arguments

Details