binPromoterAnnotation: Build binned promoter annotation for TSS enrichment

In mireia-bioinfo/meowmics: What the Package Does (One Line, Title Case)

Build binned promoter annotation for TSS enrichment

Description

Build binned promoter annotation for TSS enrichment

Usage

binPromoterAnnotation(
  scope = 2000,
  bin = 10,
  build = "hg38",
  out_format = "saf",
  genes = NULL
)

Arguments

scope	Integer indicating how many base pairs upstream and downstream to extend the promoter region. Returned window width will be scope*2. Default: 2Kb.
bin	Integer indicating the size of the bins. Default: 10 bp.
build	Name of the build to use to extract promoter coordinates. Can be either hg38 (default) or hg19.
out_format	Output format, either "saf" or "granges".
genes	Genes, as outputed by obtainCodingGenes, that is: a GRanges object with one mcol named GeneID which is a unique identifyer for the region.

Value

Either a SAF of GRanges containing binned promoter regions.

mireia-bioinfo/meowmics documentation built on July 29, 2023, 10 p.m.