visualizeGene {sesame}R Documentation

Visualize Gene

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", "MM285"),
  upstream = 2000,
  dwstream = 2000,
  refversion = c("hg38", "hg19", "mm10"),
  ...
)

Arguments

geneName

gene name

betas

beta value matrix (row: probes, column: samples)

platform

HM450, EPIC, or MM285 (default)

upstream

distance to extend upstream

dwstream

distance to extend downstream

refversion

hg19, hg38, or mm10 (default)

...

additional options, see visualizeRegion

Value

None

Examples

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

[Package sesame version 1.12.9 Index]