RnBeads (version 1.4.0)

rnb.plot.betadistribution.sampleGroups: rnb.plot.betadistribution.sampleGroups

Description

Plots beta value distrubions given a sample grouping.

Usage

rnb.plot.betadistribution.sampleGroups(beta.matrix, sample.group.inds, annotation = "Group", 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.

sample.group.inds

Named list that contains indices for the samples contained in the groups in beta.matrix. The number of groups is determined by the length of the list, and its names are used as group names.

annotation

Name of the annotation being visualized, in the form of a character vector of length 1.

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

See Also

rnb.plot.betadistribution.probeCategories

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
meth.mat <- meth(rnb.set.example)
sample.groups <- rnb.sample.groups(rnb.set.example)[[1]]
rnb.plot.betadistribution.sampleGroups(meth.mat,sample.groups)