rnb.plot.betadistribution.probeCategories {RnBeads} | R Documentation

## rnb.plot.betadistribution.probeCategories

### Description

plot beta value distrubions given probe categories

### Usage

    rnb.plot.betadistribution.probeCategories(beta.matrix, probe.cat,
      annotation = "Group", color.legend = NULL, log.str = NULL,
      points.per.group = rnb.getOption("distribution.subsample"))

### Arguments

`beta.matrix` | Beta values in the form of a non-empty `matrix` of type `double`. Rows in this matrix must correspond to Infinium probes, and columns - to samples.
`probe.cat` | `factor` vector of length `nrow(beta.matrix)` corresponding to the probe categories.
`annotation` | Name of the annotation being visualized, in the form of a `character` vector of length 1.
`color.legend` | Color legend to use in the form of a `character` vector with element names. The values in this vector should encode colors. All values in `probe.cat` must be present in the names of this color legend. If this parameter is `NULL`, a default color legend is be constructed.
`log.str` | string specifying more details for the log file
`points.per.group` | the targeted number of points per group. Set this to a value < 1 to disable subsampling. More information in the Details section of `rnb.step.betadistribution`

### Value

The plot as a `ggplot2` object.

### Author(s)

Fabian Mueller

### See Also

rnb.plot.betadistribution.sampleGroups

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    logger.start(fname=NA)
    meth.mat <- meth(rnb.set.example)
    probe.types <- annotation(rnb.set.example)[, "Design"]
    rnb.plot.betadistribution.probeCategories(meth.mat,probe.types,annotation="Infinium probe type")

[Package RnBeads version 1.10.8 Index]