rnb.plot.biseq.coverage

Description

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

Usage

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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

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