PathwayVote (version 0.1.3)

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

Description

Create an expression quantitative trait methylation (eQTM) object

Usage

create_eQTM(data, metadata = list())

Value

An eQTM object.

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).

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)