getBioRegion: getBioRegion

In YuLab-SMU/ChIPseeker: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

getBioRegion

Description

prepare a bioregion of selected feature

Usage

getBioRegion(
  TxDb = NULL,
  upstream = 1000,
  downstream = 1000,
  by = "gene",
  type = "start_site"
)

Arguments

TxDb	TxDb
upstream	upstream from start site or end site
downstream	downstream from start site or end site
by	one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR', 'UTR'
type	one of "start_site", "end_site", "body"

Details

this function combined previous functions getPromoters(), getBioRegion() and getGeneBody() in order to solve the following issues.

(1) https://github.com/GuangchuangYu/ChIPseeker/issues/16

(2) https://github.com/GuangchuangYu/ChIPseeker/issues/87

The getBioRegion() function can prevoid a region of interest from txdb object. There are three kinds of regions, start_site, end_site and body.

We take transcript region to expain the differences of these three regions. tx: chr1 1000 1400.

body region refers to the 1000-1400bp.

start_site region with upstream = 100, downstream = 100 refers to 900-1100bp.

end_site region with upstream = 100, downstream = 100 refers to 1300-1500bp.

Value

GRanges object

Author(s)

Guangchuang Yu, Ming L

YuLab-SMU/ChIPseeker documentation built on Nov. 2, 2024, 1:45 p.m.