rnb.plot.control.barplot {RnBeads} | R Documentation

## 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 `TRUE`substitute 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)

[Package RnBeads version 2.12.2 Index]