ELMER (version 1.4.2)

GetNearGenes: GetNearGenes to collect nearby genes for one locus.

Description

GetNearGenes is a function to collect equal number of gene on each side of one locus.

Usage

GetNearGenes(geneAnnot = NULL, TRange = NULL, geneNum = 20, cores = NULL)

Arguments

geneAnnot

A GRange object contains coordinates of promoter for human genome.

TRange

A GRange object contains coordinates of a list of target loci.

geneNum

A number determines how many gene will be collected totally. Then the number devided by 2 is the number of genes collected from each side of targets (number shoule be even) Default to 20.

cores

A interger which defines the number of cores to be used in parallel process. Default is NULL: no parallel process.

Value

A data frame of nearby genes' information: genes' IDs, genes' symbols, distance with target and side to which the gene locate to the target.

References

Yao L, Shen H, Laird PW, Farnham PJ,Berman BP: Inferring Regulatory Element Landscapes and Transcription Factor Networks from Cancer Methylomes. in revision of Genome Biology

Examples

geneAnnot <- txs(TSS=list(upstream=0, downstream=0))
probe <- GRanges(seqnames = c("chr1","chr2"),
range=IRanges(start = c(16058489,236417627), end= c(16058489,236417627)),
name= c("cg18108049","cg17125141"))
NearbyGenes <- GetNearGenes(geneNum=20,geneAnnot=geneAnnot,TRange=probe)