visualizeProbes {sesame}R Documentation

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 = 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')

[Package sesame version 1.2.0 Index]