get_promoter_avg {MethReg} | R Documentation

## 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)

[Package MethReg version 1.4.0 Index]