get_promoter_avg: Summarize promoter DNA methylation beta values by mean.

In TransBioInfoLab/MethReg: Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

Summarize promoter DNA methylation beta values by mean.

Description

First, identify gene promoter regions (default +-2Kkb around TSS). Then, for each promoter region calculate the mean DNA methylation of probes overlapping the region.

Usage

get_promoter_avg(
  dnam,
  genome,
  arrayType,
  cores = 1,
  upstream.dist.tss = 2000,
  downstream.dist.tss = 2000,
  verbose = FALSE
)

Arguments

dnam	A DNA methylation matrix or a SummarizedExperiment object
genome	Human genome of reference hg38 or hg19
arrayType	DNA methylation array type (450k or EPIC)
cores	A integer number to use multiple cores. Default 1 core.
upstream.dist.tss	Number of base pairs (bp) upstream of TSS to consider as promoter regions
downstream.dist.tss	Number of base pairs (bp) downstream of TSS to consider as promoter regions
verbose	A logical argument indicating if messages output should be provided.

Value

A RangedSummarizedExperiment with promoter region and mean beta-values of CpGs within it. Metadata will provide the promoter gene region and gene informations.

Examples

## Not run: 
  data("dna.met.chr21")
  promoter.avg <- get_promoter_avg(
     dnam = dna.met.chr21,
     genome = "hg19",
     arrayType = "450k"
)

## End(Not run)

TransBioInfoLab/MethReg documentation built on July 28, 2023, 9:17 p.m.