LICMEpigenetics

Provides easy to use, objective oriented functions for preprocessing methylation data produced by an Illumina Infinium BeadChip and detecting differentially methylated positions and regions within the DNA.

Installation

You can install the released version of LICMEpigenetics from Github with:

library(devtools)
devtools::install_github("LICMLeuven/LICMEpigenetics")

Example

This is a basic example which shows you how to preprocess methylation data starting from idat files and find the differentially methylated positions (DMPs):

library(LICMEpigenetics)
library(dplyr)

# Setup
set.seed(99999)
base_dir <- system.file("extdata", package="minfiDataEPIC") # path to idat files or folders
cat_vars = c("cat_1") # generic categorical name

# Preprocessing methylation data
preprocessed_set <- Make_RGset(base_dir, name="test") %>% # import idats
  ProbeNormalisation() %>% # Functional normalisation using funnorm
  ProbeExclusion() %>% # Exclude CPG, SBE, sex probes and probes not exceeding background signal
  ConvertSet() # convert genomic methyl set into beta set.

# DMP calculation
Random_AdjustmentVars <- data.frame(replicate(1, sample(0:1, 3, rep=TRUE)))
colnames(Random_AdjustmentVars) <- cat_vars

LimmaOutput <- DMP_limma(preprocessed_set$mset, Random_AdjustmentVars, cat_vars=cat_vars, Group="cat_1")