RnBeads (version 1.4.0)

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

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.

Examples

library(RnBeads.hg19)
data(small.example.object)
control.meta.data <- rnb.get.annotation("controls450")
ctrl.probe<-paste0(unique(control.meta.data[["Target"]])[4], ".5")
print(ctrl.probe) # EXTENSION.5
rnb.control.barplot(rnb.set.example, ctrl.probe)