visualizeRegion: Visualize Region

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

The function takes a genomic coordinate (chromosome, start and end) and a beta value matrix (probes on the row and samples on the column). It plots the beta values as a heatmap for all probes falling into the genomic region. If 'draw=TRUE' the function returns the plotted grid graphics object. Otherwise, the selected beta value matrix is returned. 'cluster.samples=TRUE/FALSE' controls whether hierarchical clustering is applied to the subset beta value matrix.

Usage

visualizeRegion(
  chrm,
  plt.beg,
  plt.end,
  betas,
  platform = c("EPIC", "HM450"),
  refversion = c("hg38", "hg19"),
  sample.name.fontsize = 10,
  heat.height = NULL,
  draw = TRUE,
  show.sampleNames = TRUE,
  show.samples.n = NULL,
  show.probeNames = TRUE,
  cluster.samples = FALSE,
  nprobes.max = 1000,
  na.rm = FALSE,
  dmin = 0,
  dmax = 1
)

Arguments

chrm	chromosome
plt.beg	begin of the region
plt.end	end of the region
betas	beta value matrix (row: probes, column: samples)
platform	EPIC or HM450
refversion	hg38 or hg19
sample.name.fontsize	sample name font size
heat.height	heatmap height (auto inferred based on rows)
draw	draw figure or return betas
show.sampleNames	whether to show sample names
show.samples.n	number of samples to show (default: all)
show.probeNames	whether to show probe names
cluster.samples	whether to cluster samples
nprobes.max	maximum number of probes to plot
na.rm	remove probes with all NA.
dmin	data min
dmax	data max

Value

graphics or a matrix containing the captured beta values

Examples

betas <- sesameDataGet('HM450.76.TCGA.matched')$betas
visualizeRegion('chr20', 44648623, 44652152, betas, 'HM450')

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