visualizeProbes: Visualize Region that Contains the Specified Probes

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

Visualize the beta value in heatmaps for the genomic region containing specified probes. The function works only if specified probes can be spanned by a single genomic region. The region can cover more probes than specified. Hence the plotting heatmap may encompass more probes. The function takes as input a string vector of probe IDs (cg/ch/rs-numbers). if draw is FALSE, the function returns the subset beta value matrix otherwise it returns the grid graphics object.

Usage

visualizeProbes(
  probeNames,
  betas,
  platform = c("EPIC", "HM450"),
  refversion = c("hg38", "hg19"),
  upstream = 1000,
  dwstream = 1000,
  ...
)

Arguments

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

Value

None

Examples

betas <- sesameDataGet('HM450.76.TCGA.matched')$betas
visualizeProbes(c('cg22316575', 'cg16084772', 'cg20622019'), betas, 'HM450')

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