visualizeProbes: Visualize Region that Contains the Specified Probes

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Visualize Region that Contains the Specified Probes

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 = NULL,
  genome = NULL,
  upstream = 1000,
  dwstream = 1000,
  ...
)

Arguments

probeNames	probe names
betas	beta value matrix (row: probes, column: samples)
platform	HM450, EPIC or MM285 (default)
genome	hg19, hg38 or mm10 (default)
upstream	distance to extend upstream
dwstream	distance to extend downstream
...	additional options, see visualizeRegion and assemble_plots

Value

None

Examples

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

zwdzwd/sesame documentation built on Nov. 11, 2024, 9:33 a.m.