get_promoter_avg {MethReg} | R Documentation |
First, identify gene promoter regions (default +-2Kkb around TSS). Then, for each promoter region calculate the mean DNA methylation of probes overlapping the region.
get_promoter_avg( dnam, genome, arrayType, cores = 1, upstream.dist.tss = 2000, downstream.dist.tss = 2000, verbose = FALSE )
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. |
A RangedSummarizedExperiment with promoter region and mean beta-values of CpGs within it. Metadata will provide the promoter gene region and gene informations.
## Not run: data("dna.met.chr21") promoter.avg <- get_promoter_avg( dnam = dna.met.chr21, genome = "hg19", arrayType = "450k" ) ## End(Not run)