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