AMR_search: Find AMR

In jumentib/hdmax2: High Dimensionnal Mediation Analysis

Description

To identify aggregated methylated regions (AMR) using a modified comb-p method.

Usage

AMR_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
...	see help of combp of ENmix package

Details

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

Value

A set of selected AMRs.

Author(s)

Basile Jumentier

Examples

# library(hdma2)
#
# Run mEWAS
#
# res <- mEWAS(X = example$X, Y = example$Y, M = example$M, K = 5)
#
# Keep latent factors for mediation
#
# U <- res$U
#
# Run max2
#
# res <- max2(pval1 = res$pValue[, 1], pval2 = res$pValue[, 2])
#
# lauch AMR_search
#
# res <- AMR_search(chr = example$annotation$chr,
#                   start = example$annotation$start,
#                   end = example$annotation$end,
#                   pval = res$pval,
#                   cpg = example$annotation$cpg, nCores = 1)
#

jumentib/hdmax2 documentation built on Feb. 25, 2022, 12:58 p.m.