DMR {sesame}R Documentation

Find Differentially Methylated Region (DMR)

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,
  cf,
  platform = NULL,
  refversion = NULL,
  dist.cutoff = NULL,
  seg.per.locus = 0.5
)

Arguments

betas

beta values for distance calculation

cf

coefficient table from DML or DMLShrinkage

platform

EPIC, HM450, MM285, ...

refversion

hg38, hg19, mm10, ...

dist.cutoff

distance cutoff (default to use dist.cutoff.quantile)

seg.per.locus

number of segments per locus higher value leads to more segments

Value

coefficient table with segment ID and segment P-value

Examples


sesameDataCache("HM450") # in case not done yet

data <- sesameDataGet('HM450.76.TCGA.matched')
cf_list = summaryExtractCfList(DML(data$betas, ~type, meta=data$sampleInfo))
cf_list = DMR(data$betas, cf_list$typeTumour)

[Package sesame version 1.8.10 Index]