rnb.plot.control.barplot: rnb.plot.control.barplot

In RnBeads: RnBeads

Description

Per-sample bar plots of Illumina HumanMethylation control probes

Usage

rnb.plot.control.barplot(
  rnb.set,
  probe,
  sample.subset = 1:length(samples(rnb.set)),
  writeToFile = FALSE,
  numeric.names = FALSE,
  name.prefix = NULL,
  verbose = FALSE,
  ...
)

Arguments

rnb.set	RnBeadRawSet or RnBeadSet object with valid quality control information
probe	exact id of the control probe consisting of the control probe type (see rnb.plot.control.boxplot)
sample.subset	an integer vector specifying the subset of samples for which the plotting should be performed
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
name.prefix	in case writeToFile is TRUE, a character singleton specifying a prefix to the variable part of the image file names
verbose	if TRUE additional diagnostic output is generated
...	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

Examples

library(RnBeads.hg19)
data(small.example.object)
control.meta.data <- rnb.get.annotation("controls450")
ctrl.probe<-paste0(unique(control.meta.data[["Target"]])[4], ".3")
print(ctrl.probe) # EXTENSION.3
rnb.plot.control.barplot(rnb.set.example, ctrl.probe)

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