DMR: Find Differentially Methylated Region (DMR)

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

This subroutine uses Euclidean distance to group CpGs and then combine p-values for each segment. The function performs DML test first if cf is NULL. It groups the probe testing results into differential methylated regions in a coefficient table with additional columns designating the segment ID and statistical significance (P-value) testing the segment.

Usage

DMR(
  betas,
  sample.data = NULL,
  formula = NULL,
  cf = NULL,
  dist.cutoff = NULL,
  seg.per.locus = 0.5,
  platform = c("EPIC", "HM450"),
  refversion = c("hg38", "hg19"),
  ...
)

Arguments

betas	beta values for distance calculation
sample.data	data frame for sample information, column names are predictor variables (e.g., sex, age, treatment, tumor/normal etc) and are referenced in formula. Rows are samples.
formula	formula
cf	coefficient table from diffMeth, when NULL will be computed from beta. If cf is given, sample.data and formula are ignored.
dist.cutoff	distance cutoff (default to use dist.cutoff.quantile)
seg.per.locus	number of segments per locus higher value leads to more segments
platform	EPIC or HM450
refversion	hg38 or hg19
...	additional parameters to DML

Value

coefficient table with segment ID and segment P-value

Examples

data <- sesameDataGet('HM450.76.TCGA.matched')
cf <- DMR(data$betas, data$sampleInfo, ~type)

sesame documentation built on Nov. 15, 2020, 2:08 a.m.