getFunctionalGenes: The getFunctionalGenes function

In gevaertlab/EpiMix: EpiMix: an integrative tool for the population-level analysis of DNA methylation

The getFunctionalGenes function

Description

Helper function to assess if the methylation of a probe is reversely correlated with the expression of its nearby genes.

Usage

getFunctionalGenes(
  target.probe,
  target.genes,
  MET_matrix,
  gene.expression.data,
  ProbeAnnotation,
  correlation = "negative",
  raw.pvalue.threshold = 0.05,
  adjusted.pvalue.threshold = 0.01
)

Arguments

target.probe	character string indicating the probe to be evaluated.
target.genes	character vector indicating the nearby genes of the target probe.
MET_matrix	methylation data matrix for CpGs from group.1 and group.2.
gene.expression.data	gene expression data matrix.
ProbeAnnotation	GRange object of CpG probe annotation.
raw.pvalue.threshold	raw p value from testing DNA methylation and gene expression
adjusted.pvalue.threshold	adjusted p value from testing DNA methylation and gene expression

Details

This function is probe-centered, which is used in the enhancer mode and the miRNA mode of EpiMix.

Value

dataframe with functional probe-gene pair and p values from the Wilcoxon test for methylation and gene expression.

Examples

data(Sample_EpiMixResults_Enhancer)
data(mRNA.data)
EpiMixResults <- Sample_EpiMixResults_Enhancer
target.probe <- EpiMixResults$FunctionalPairs$Probe[1]
target.genes <- EpiMixResults$FunctionalPairs$Gene
MET_matrix <- EpiMixResults$MethylationStates
ProbeAnnotation <- ExperimentHub::ExperimentHub()[["EH3675"]]
res <- getFunctionalGenes(target.probe, target.genes, MET_matrix, mRNA.data, ProbeAnnotation)

gevaertlab/EpiMix documentation built on July 20, 2023, 9:28 a.m.