getUCSC: Get nearest genes for the window of the upstream/downstream...

In NoRCE: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

Description

When downstream = 0 / upstream = 0, function converts bed formated regions to HUGO genes

Usage

getUCSC(
  bedfile,
  upstream,
  downstream,
  org_assembly = c("hg19", "hg38", "mm10", "dre10", "rn6", "dm6", "ce11", "sc3")
)

Arguments

bedfile	Bed formated input gene regions
upstream	Maximum upstream distance from the transcription start region of the input gene
downstream	Maximum downstream distance from the transcription end region of the input gene
org_assembly	genomee assembly of interest for the analysis. Possible assemblies are "mm10" for mouse, "dre10" for zebrafish, "rn6" for rat, "dm6" for fruit fly, "ce11" for worm, "sc3" for yeast, "hg19" and "hg38" for human

Value

genes

Examples

regions<-system.file("extdata", "ncRegion.txt", package = "NoRCE")
regionNC <- rtracklayer::import(regions, format = "BED")

neighbour <- getUCSC(bedfile = regionNC,
                     upstream = 1000,
                     downstream = 1000,
                     org_assembly = 'hg19')

NoRCE documentation built on Nov. 8, 2020, 7:17 p.m.