visualizeRegion {sesame} | R Documentation |
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.
visualizeRegion( chrm, plt.beg, plt.end, betas, platform = c("EPIC", "HM450", "MM285"), refversion = c("hg38", "hg19", "mm10"), 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 )
chrm |
chromosome |
plt.beg |
begin of the region |
plt.end |
end of the region |
betas |
beta value matrix (row: probes, column: samples) |
platform |
EPIC, HM450, or MM285 |
refversion |
hg38, hg19, or mm10 |
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 |
graphics or a matrix containing the captured beta values
betas <- sesameDataGet('HM450.76.TCGA.matched')$betas visualizeRegion('chr20', 44648623, 44652152, betas, 'HM450')