meta_regions: Metagene Regions

In manschmi/RMetaTools: Tools For Metagene Analysis

Description

Creates regions for metagene analysis.

Usage

meta_regions(bed, anchor = "TSS", upstream = 1000, downstream = 1000)

Arguments

bed	filename for bed file.
anchor	anchor point TSS, TES, center or NULL (default='TSS')
upstream	bp upstream of anchor (default=1000)
downstream	bp downstream of anchor (default=1000)

Details

Loads the bed file. If anchor is NULL, returns region from TSS-upstream to TES+downstream. If anchor, extracts the position of the anchor point and creates ranges from x bp upstream to x bp downstream of the anchor point.

Value

GRanges with regions.

Examples

bedfile <- system.file("extdata", "Chen_PROMPT_TSSs_liftedTohg38.bed", package = "RMetaTools")
meta_regions(bedfile, 'TSS', 1000, 5000)

manschmi/RMetaTools documentation built on Dec. 14, 2021, 4:33 a.m.