DMR_search: Find DMR

In jumentib/highmed: High Dimensionnal Mediation Analysis

Description

To identify differentially methylated regions using a modified comb-p method.

Usage

DMR_search(chr, start, end, pval, cpg, ...)

Arguments

chr	chromosomes
start	chromosomal position of markers (start)
end	chromosomal position of markers (end)
pval	pValues for each markers, from the max2 function
cpg	name of each markers
...	argument of the combp function from the ENmix package

Details

The function will use a modified comb-p method to identify differentially methylated regions (DMRs).

Value

A set of selected DMRs.

Author(s)

Basile Jumentier

Examples

library(highmed)

# Run multivariate EWAS

res <- multivariate_EWAS(X = example$X, Y = example$Y, M = example$M, K = 5)

# Keep latent factors for univariate mediation

U <- res$U

# Run max2

res <- max2(pval1 = res$pValue[, 1], pval2 = res$pValue[, 2])

# lauch DMR_search

res <- DMR_search(chr = example$annotation$chr,
                  start = example$annotation$start,
                  end = example$annotation$end,
                  pval = res$pval,
                  cpg = example$annotation$cpg, nCores = 1)

jumentib/highmed documentation built on Sept. 3, 2020, 2 p.m.