rnb.plot.biseq.coverage: rnb.plot.biseq.coverage

In RnBeads: RnBeads

Description

Plots the sequencing coverage of the RnBiseqSet object across the genomic coordinate

Usage

rnb.plot.biseq.coverage(
  rnbs.set,
  sample,
  type = "sites",
  writeToFile = FALSE,
  numeric.names = FALSE,
  covg.lists = NULL,
  ...
)

Arguments

rnbs.set	RnBiseqSet object
sample	unique sample identifier. In case rnb.getOption("identifiers.column") is not NULL, sample should attain values from the corresponding column, or colnames(meth(rnb.set)) otherwise
type	character singleton. If site the coverage information is plotted for each methylation site. Otherwise should be one of the regions returned by rnb.region.types
writeToFile	flag specifying whether the output should be saved as ReportPlot
numeric.names	if TRUE and writeToFile is TRUEsubstitute the plot options in the plot file name with digits
covg.lists	if available, the output of rnb.execute.quality
...	other arguments to createReportPlot

Value

plot as an object of type ReportPlot if writeToFile is TRUE and of class ggplot otherwise.

Author(s)

Pavlo Lutsik

RnBeads documentation built on March 3, 2021, 2 a.m.