getNearToIntron {NoRCE} | R Documentation |
Get only those neighbouring genes that fall within intron region
getNearToIntron( bedfile, upstream, downstream, org_assembly = c("hg19", "hg38", "mm10", "dre10", "rn6", "dm6", "ce11", "sc3") )
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 |
genes
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')