getProbesByGene: Get Probes by Gene

Description Usage Arguments Value Examples

View source: R/visualize.R

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

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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

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

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