generateFunctionalPairs: The generateFunctionalPairs function

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

The generateFunctionalPairs function

Description

Wrapper function to get functional CpG-gene pairs, used for Regular, miRNA and lncRNA modes

Usage

generateFunctionalPairs(
  MET_matrix,
  control.names,
  gene.expression.data,
  ProbeAnnotation,
  raw.pvalue.threshold,
  adjusted.pvalue.threshold,
  cores,
  mode = "Regular",
  correlation = "negative"
)

Arguments

MET_matrix	matrix of methylation states
control.names	character vector indicating the samples names in the control group
gene.expression.data	matrix of gene expression data
ProbeAnnotation	dataframe of probe annotation
raw.pvalue.threshold	raw p value threshold
adjusted.pvalue.threshold	adjusted p value threshold
cores	number of computational cores
mode	character string indicating the analytic mode
correlation	the expected relationship between DNAme and gene expression

Value

a dataframe of functional CpG-gene matrix

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