denv_data

A dataset containing neutralization titer data for Dengue virus. This data can be used to
create antigenic maps and explore the antigenic relationships between different DENV strains.

datasets

An implementation of the TopoLow algorithm, a novel, physics-inspired method for
antigenic cartography. TopoLow addresses significant challenges in mapping antigenic relationships,
especially from sparse and noisy experimental data. The package transforms cross-reactivity and
binding affinity measurements into accurate spatial representations in a phenotype space.
Key features include:
* Robust Mapping from Sparse Data: Effectively creates complete and consistent maps even with high
proportions of missing data (e.g., >95%).
* Physics-Inspired Optimization: Models antigens as particles connected by springs (for measured
interactions) and subject to repulsive forces (for missing interactions), reducing the need for
complex gradient computations.
* Automatic Dimensionality Detection: Employs a likelihood-based approach to determine the optimal
number of dimensions for the antigenic map, avoiding distortions common in methods with fixed low dimensions.
* Noise and Bias Reduction: Naturally mitigates experimental noise and bias through its network-based,
error-dampening mechanism.
* Antigenic Velocity Calculation: Introduces and quantifies "antigenic velocity," a vector that describes
the rate and direction of antigenic drift for each pathogen isolate. This can help identify cluster
transitions and potential lineage replacements.
* Broad Applicability: Analyzes data from various pathogens, including influenza, HIV, and Dengue viruses.
It can be applied to any continuous and relational phenotype under directional selection pressure.
Methods are described in Arhami and Rohani (2025) <doi:10.1093/bioinformatics/btaf372>.

Omid Arhami

topolow

Antigenic Mapping and Antigenic Velocity Algorithm

denv_data function

A data frame with the following columns:<dl>
<dt>virus_strain</dt>
<dd>Character, the name of the virus strain.</dd><dt>serum_strain</dt>
<dd>Character, the name of the serum strain.</dd><dt>titer</dt>
<dd>Character, the neutralization titer value. May include values like '&lt;10' or '&gt;1280'.</dd><dt>virusYear</dt>
<dd>Numeric, the year the virus was isolated.</dd><dt>serumYear</dt>
<dd>Numeric, the year the serum was collected.</dd><dt>cluster</dt>
<dd>Factor, the cluster or serotype assignment for the strains.</dd><dt>color</dt>
<dd>Character, a color associated with the cluster for plotting.</dd>
</dl>

Format

Dengue Virus (DENV) Titer Data — denv_data

A data frame with the following columns:<dl>
<dt>virus_strain</dt>
<dd>Character, the name of the virus strain.</dd>

<dt>serum_strain</dt>
<dd>Character, the name of the serum strain.</dd>

<dt>titer</dt>
<dd>Character, the neutralization titer value. May include values like '&lt;10' or '&gt;1280'.</dd>

<dt>virusYear</dt>
<dd>Numeric, the year the virus was isolated.</dd>

<dt>serumYear</dt>
<dd>Numeric, the year the serum was collected.</dd>

<dt>cluster</dt>
<dd>Factor, the cluster or serotype assignment for the strains.</dd>

<dt>color</dt>
<dd>Character, a color associated with the cluster for plotting.</dd>


</dl>

denv_data: Dengue Virus (DENV) Titer Data

Description

Usage

Arguments

Format