DMR: Find Differentially Methylated Region (DMR)

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

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,
  smry,
  contrast,
  platform = NULL,
  probe.coords = NULL,
  dist.cutoff = NULL,
  seg.per.locus = 0.5
)

Arguments

betas	beta values for distance calculation
smry	DML
contrast	the pair-wise comparison or contrast check colnames(attr(smry, "model.matrix")) if uncertain
platform	EPIC, HM450, MM285, ...
probe.coords	GRanges object that defines CG coordinates if NULL (default), then the default genome assembly is used. Default genome is given by, e.g., sesameData_check_genome(NULL, "EPIC") For additional mapping, download the GRanges object from http://zwdzwd.github.io/InfiniumAnnotation and provide the following argument ..., probe.coords = sesameAnno_buildManifestGRanges("downloaded_file"),... to this function.
dist.cutoff	cutoff of beta value differences for two neighboring CGs to be considered the same DMR (by default it's determined using the quantile function on seg.per.locus)
seg.per.locus	number of segments per locus higher value leads to more segments

Value

coefficient table with segment ID and segment P-value each row is a locus, multiple loci may share a segment ID if they are merged to the same segment. Records are ordered by Seg_Est.

Examples

sesameDataCache() # in case not done yet

data <- sesameDataGet('HM450.76.TCGA.matched')
smry <- DML(data$betas[1:1000,], ~type, meta=data$sampleInfo)
colnames(attr(smry, "model.matrix")) # pick a contrast from here
## showing on a small set of 100 CGs
merged_segs <- DMR(data$betas[1:1000,], smry, "typeTumour", platform="HM450")

sesameDataGet_resetEnv()

zwdzwd/sesame documentation built on Dec. 21, 2024, 1:20 p.m.