getProbesByGene: Get Probes by Gene

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

Get probes mapped to a gene. All transcripts for the gene are considered. The function takes a gene name as appears in UCSC RefGene database. The platform and reference genome build can be changed with 'platform' and 'refversion' options. The function returns a vector of probes that falls into the given gene.

Usage

getProbesByGene(
  geneName,
  platform = c("EPIC", "HM450"),
  upstream = 0,
  dwstream = 0,
  refversion = c("hg38", "hg19")
)

Arguments

geneName	gene name
platform	EPIC or HM450
upstream	number of bases to expand upstream of target gene
dwstream	number of bases to expand downstream of target gene
refversion	hg38 or hg19

Value

probes that fall into the given gene

Examples

probes <- getProbesByGene('CDKN2A', upstream=500, dwstream=500)

sesame documentation built on Nov. 15, 2020, 2:08 a.m.