getData

getData,eQTM-method

Retrieve the eQTM data.frame from an eQTM object.

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

getData function

<dl><dt>object</dt>
<dd>An eQTM object.</dd></dl>

Arguments

Get expression quantitative trait methylation (eQTM) Data — getData

<dl>

<dt>object</dt>
<dd>An eQTM object.</dd>

</dl>

getData: Get expression quantitative trait methylation (eQTM) Data

Description

Usage

Value

Arguments