visualizeProbes {sesame} | R Documentation |
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.
visualizeProbes( probeNames, betas, platform = c("EPIC", "HM450", "MM285"), refversion = c("hg38", "hg19", "mm10"), upstream = 1000, dwstream = 1000, ... )
probeNames |
probe names |
betas |
beta value matrix (row: probes, column: samples) |
platform |
HM450, EPIC or MM285 (default) |
refversion |
hg19, hg38 or mm10 (default) |
upstream |
distance to extend upstream |
dwstream |
distance to extend downstream |
... |
additional options, see visualizeRegion |
None
betas <- sesameDataGet('HM450.76.TCGA.matched')$betas visualizeProbes(c('cg22316575', 'cg16084772', 'cg20622019'), betas, 'HM450')