GetNearGenes: GetNearGenes to collect nearby genes for one locus.

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

GetNearGenes is a function to collect equal number of gene on each side of one locus. It can receite either multi Assay Experiment with both DNA methylation and gene Expression matrix and the names of probes to select nearby genes, or it can receive two granges objects TRange and geneAnnot.

Usage

GetNearGenes(
  data = NULL,
  probes = NULL,
  geneAnnot = NULL,
  TRange = NULL,
  numFlankingGenes = 20
)

Arguments

data	A multi Assay Experiment with both DNA methylation and gene Expression objects
probes	Name of probes to get nearby genes (it should be rownames of the DNA methylation object in the data argument object)
geneAnnot	A GRange object or Summarized Experiment object that contains coordinates of promoters for human genome.
TRange	A GRange object or Summarized Experiment object that contains coordinates of a list of targets loci.
numFlankingGenes	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.

Value

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

References

Yao, Lijing, et al. "Inferring regulatory element landscapes and transcription factor networks from cancer methylomes." Genome biology 16.1 (2015): 1.

Examples

geneAnnot <- 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 <- GetNearGenes(numFlankingGenes = 20,geneAnnot=geneAnnot,TRange=probe)

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.