getNearToIntron: Get only those neighbouring genes that fall within intron...

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

Description

Get only those neighbouring genes that fall within intron region

Usage

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

Arguments

bedfile	Bed file
upstream	upstream distance
downstream	downstream distance
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")

r<-getNearToExon(bedfile = regionNC,
                 upstream = 1000,
                 downstream = 2000,
                 org_assembly = 'hg19')

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