getRegionNearGenes {ELMER} | R Documentation |
Auxiliary function for GetNearGenes This will get the closest genes (n=numFlankingGenes) for a target region (TRange) based on a genome of refenrece gene annotation (geneAnnot). If the transcript level annotation (tssAnnot) is provided the Distance will be updated to the distance to the nearest TSS.
getRegionNearGenes( TRange = NULL, numFlankingGenes = 20, geneAnnot = NULL, tssAnnot = NULL )
TRange |
A GRange object contains coordinate of targets. |
numFlankingGenes |
A number determine how many gene will be collected from each |
geneAnnot |
A GRange object contains gene coordinates of for human genome. |
tssAnnot |
A GRange object contains tss coordinates of for human genome. |
A data frame of nearby genes and information: genes' IDs, genes' symbols,
Tiago C Silva (maintainer: tiagochst@usp.br)
geneAnnot <- ELMER:::get.GRCh("hg38",as.granges = TRUE) tssAnnot <- getTSS(genome = "hg38") probe <- GenomicRanges::GRanges(seqnames = c("chr1","chr2"), range=IRanges::IRanges(start = c(16058489,236417627), end= c(16058489,236417627)), name= c("cg18108049","cg17125141")) names(probe) <- c("cg18108049","cg17125141") NearbyGenes <- getRegionNearGenes(numFlankingGenes = 20, geneAnnot = geneAnnot, TRange = probe, tssAnnot = tssAnnot)