DMR_dmrcate: Detect differentially methylated positions in the DNA using...

In GregoireCoppens/LICMEpigenetics: Processing of Epigenetic data

Detect differentially methylated positions in the DNA using the limma package.

Description

This function uses 'limma' package to generate t-values. Then it smooths out these t-statistics using gaussian kernel smoothing. The t-values that remain significant after smoothing and multiple testing, are grouped when they are within Lambda base pairs from each other. Such a group is called a Differently Methylated Region (DMR).

Usage

DMR_dmrcate(
  set,
  DMP,
  lambda = 1000,
  fdr = 0.05,
  ann_array = c(array = "IlluminaHumanMethylationEPIC", annotation = "ilmn10b2.hg19")
)

Arguments

set	Preprocessed methylation set, can be genomic methyl set or genomic ratio set.
DMP	Output from 'DMP_limma()' function.
lambda	Gaussian kernel bandwidth for smoothed-function estimation. Also informs DMR bookend definition; gaps >= lambda between significant CpG sites will be in separate DMRs. Support is truncated at 5*lambda. Default is 1000 nucleotides.
fdr	false discovery rate, default = 0.05.
ann_array	Specify whether Illumina arraytype is 'IlluminaHumanMethylation450k' or 'IlluminaHumanMethylationEPIC' and the annotation file is 'ilmn12.hg19' or "ilmn10b2.hg19"

Value

An S4 object with statistics for every DMR

• DMR - 'dmrcate()'output, a S4 object with statistics for every DMR

• DMRRanges - 'extractRanges()' output, a S4 object with Ranges from found DMRs

• annotation - 'cpg.annotate()' output, a s4 object with statistics on every CpG site.

GregoireCoppens/LICMEpigenetics documentation built on April 24, 2023, 10:02 a.m.