test_gene_expr: The test_gene_expr function

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

The test_gene_expr function

Description

Helper function to test whether the expression levels of a gene is reversely correlated with the methylation state of a probe.

Usage

test_gene_expr(
  gene,
  probe,
  DM_values,
  gene.expr.values,
  correlation = "negative"
)

Arguments

gene	character string indicating a target gene to be modeled.
probe	character string indicating a probe mapped to the target gene.
DM_values	a vector of DM values for the probe. The names of the element should be sample names.
gene.expr.values	a vector of gene expression values for the tested gene. The names of the vector are sample names.
correlation	character indicating the direction of correlation between the methylation state of the CpG site and the gene expression levels. Can be either 'negative' or 'positive'.
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

Value

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

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