getRandomGenes: The getRandomGenes function

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

The getRandomGenes function

Description

Helper function to get a set of random genes located on different chromosomes of the target CpG.

Usage

getRandomGenes(
  target.probe,
  gene.expression.data,
  ProbeAnnotation,
  genome = "hg38",
  perm = 1000
)

Arguments

target.probe	character string indicating the target CpG for generating the permutation p values.
gene.expression.data	a matrix of gene expression data.
ProbeAnnotation	GRange object of probe annotation.
genome	character string indicating the genome build version, can be either 'hg19' or 'hg38'.
perm	the number of permutation tests. Default: 1000

Value

a dataframe for the permutation genes and p values for the target CpG site.

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