DMRfinder: DMR finder

In molepi/DNAmArray: Streamlined workflow for the quality control, normalization and bias-free analysis of Illumina methylation array data - The Leiden approach

DMR finder

Description

DMR finder

Usage

DMRfinder(
  data,
  chromosome = c(1:22, "X", "Y"),
  mismatches = 3,
  icd = 1000,
  illumina = TRUE
)

Arguments

data	GRanges-class object, named vector, matrix, or data.frame
chromosome	Chromosomes as numeric or "X" or "Y"
mismatches	Number of non-significant DMPs allowed (default: 3)
icd	Inter-CpG distance (default: 1000bp)
illumina	binary indicator (default: TRUE)

Details

Algorithm to identify differentially methylated regions (DMRs) from a list of differentially methylated probes (DMPs). This was developed by Roderick Slieker and is described in "Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array" Slieker et al. (2013)

Value

GRanges-class object containing DMRs

Author(s)

R Sliecker, E.W Lameijer, and M. van Iterson

molepi/DNAmArray documentation built on Aug. 24, 2022, 1:42 p.m.