visualizeGene: Visualize Gene

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

Visualize the beta value in heatmaps for a given gene. The function takes a gene name which is taken from the UCSC refGene. It searches all the transcripts for the given gene and optionally extend the span by certain number of base pairs. The function also takes a beta value matrix with sample names on the columns and probe names on the rows. The function can also work on different genome builds (default to hg38, can be hg19).

Usage

visualizeGene(
  geneName,
  betas,
  platform = c("EPIC", "HM450"),
  upstream = 2000,
  dwstream = 2000,
  refversion = c("hg38", "hg19"),
  ...
)

Arguments

geneName	gene name
betas	beta value matrix (row: probes, column: samples)
platform	HM450 or EPIC (default)
upstream	distance to extend upstream
dwstream	distance to extend downstream
refversion	hg19 or hg38 (default)
...	additional options, see visualizeRegion

Value

None

Examples

betas <- sesameDataGet('HM450.76.TCGA.matched')$betas
visualizeGene('ADA', betas, 'HM450')

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