RnBeads (version 1.4.0)

rnb.step.betadistribution: rnb.step.betadistribution

Description

Computes the distributions of beta values across various sample groups and adds a corresponding section to the report.

Usage

rnb.step.betadistribution(rnb.set, report, columns = rnb.getOption("exploratory.columns"), points.per.group = rnb.getOption("distribution.subsample"))

Arguments

rnb.set

HumanMethylation450K dataset as an object of type RnBSet.

report

Report to contain the methylation deviation section. This must be an object of type Report.

columns

Optional; predefined column names (in the form of a character vector) or indices (an integer vector) in the sample annotation table. Only these columns are considered for grouping samples and defining profiles. All other columns in the phenotype table are ignored.

points.per.group

the targeted number of points (T) per group. Set this to a value < 1 to disable subsampling. More information in the Details section

Value

The modified report.

Details

If subsampling is enabled (i.e. points.per.group>0), observations per group are subsampled according to the following procedure: Given K groups and numbers of observed beta values per group N_1,...,N_K, and the target number of points per group T: the total number of points N = sum(N_1,...,N_K) is computed Afterwards the proportions p_k = N_k/N is computed and from each group, S_k = p_k*(K*T) observations are randomly selected from all observations belonging to group k.