eQTM-class

A class to store eQTM data for pathway analysis. eQTM stands for Expression Quantitative Trait Methylation.

Performs pathway enrichment analysis using a voting-based framework that integrates CpG–gene regulatory information from expression quantitative trait methylation (eQTM) data. For a grid of top-ranked CpGs and filtering thresholds, gene sets are generated and refined using an entropy-based pruning strategy that balances information richness, stability, and probe bias correction. In particular, gene lists dominated by genes with disproportionately high numbers of CpG mappings are penalized to mitigate active probe bias—a common artifact in methylation data analysis. Enrichment results across parameter combinations are then aggregated using a voting scheme, prioritizing pathways that are consistently recovered under diverse settings and robust to parameter perturbations.

Yinan Zheng

PathwayVote

Robust Pathway Enrichment for DNA Methylation Studies Using
Ensemble Voting

eQTM-class function

<dl>
<dt><code>data</code></dt>
<dd>A data.frame containing eQTM data with columns: cpg, statistics, p_value, distance, and at least one of entrez or ensembl.</dd></dl>
<dt><code>metadata</code></dt>
<dd>A list of metadata (e.g., data source, time point). Reserved for future use.</dd>

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Expression quantitative trait methylation (eQTM) Class — eQTM-class

<dl>
<dt><code>data</code></dt>
<dd>A data.frame containing eQTM data with columns: cpg, statistics, p_value, distance, and at least one of entrez or ensembl.</dd>


<dt><code>metadata</code></dt>
<dd>A list of metadata (e.g., data source, time point). Reserved for future use.</dd>


</dl>

eQTM-class: Expression quantitative trait methylation (eQTM) Class

Description

Arguments

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