getNearToExon: Get only those neighbouring genes that fall within exon...

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

Description

Get only those neighbouring genes that fall within exon region

Usage

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

Arguments

bedfile	Input bed formated file
upstream	Maximum upstream distance from the TSS position
downstream	Maximum downstream distance from the TES position
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.