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

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")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RnBeads)
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Warning message:
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> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RnBeads/rnb.plot.betadistribution.probeCategories.Rd_%03d_medium.png", width=480, height=480)
> ### Name: rnb.plot.betadistribution.probeCategories
> ### Title: rnb.plot.betadistribution.probeCategories
> ### Aliases: rnb.plot.betadistribution.probeCategories
> 
> ### ** Examples
> 
> ## No test: 
> 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")
2016-07-06 05:00:29     0.9    INFO Density estimation ( Infinium probe type ): Groupwise retained observations after missing value removal: I:5964/5964; II:14868/14868
> ## End(No test)
> 
> 
> 
> 
> 
> dev.off()
null device 
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>