getProbesByTSS: Get Probes by Gene Transcription Start Site (TSS)

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

Get probes mapped to a TSS. 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 TSS region of the gene.

Usage

getProbesByTSS(
  geneName,
  upstream = 1500,
  dwstream = 1500,
  platform = c("EPIC", "HM450"),
  refversion = c("hg38", "hg19")
)

Arguments

geneName	gene name
upstream	the number of base pairs to expand upstream the TSS
dwstream	the number of base pairs to expand dwstream the TSS
platform	EPIC or HM450
refversion	hg38 or hg19

Value

probes that fall into the given gene

Examples

probes <- getProbesByTSS('CDKN2A')

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