create_eQTM: Create an expression quantitative trait methylation (eQTM)...

In PathwayVote: Robust Pathway Enrichment for DNA Methylation Studies Using Ensemble Voting

Create an expression quantitative trait methylation (eQTM) object

Description

Create an expression quantitative trait methylation (eQTM) object

Usage

create_eQTM(data, metadata = list())

Arguments

data

A data.frame containing eQTM data with columns: cpg, statistics, p_value, distance, and at least one of entrez or ensembl. cpg Character. CpG probe ID (e.g., "cg00000029"), representing a methylation site. statistics Numeric. Test statistic from eQTM association analysis (e.g., correlation coefficient, r-square, regression coefficient, or t-statistic). Can be positive or negative. p_value Numeric. P-value associated with the test statistic, must be between 0 and 1. distance Numeric. Genomic distance (in base pairs) between the CpG and the associated gene's transcription start site (TSS). Must be non-negative. entrez Character. Entrez gene ID of the associated gene. At least one of entrez or ensembl must be provided. ensembl Character. Ensembl gene ID of the associated gene. At least one of entrez or ensembl must be provided.

metadata

A list of metadata (optional).

Value

An eQTM object.

Examples

data <- data.frame(
  cpg = c("cg000001", "cg000002"),
  statistics = c(2.5, -1.8),
  p_value = c(0.01, 0.03),
  distance = c(50000, 80000),
  entrez = c("673", "1956")
)
eqtm_obj <- create_eQTM(data)

PathwayVote documentation built on June 25, 2025, 5:09 p.m.