rnb.step.betadistribution {RnBeads} | R Documentation

## 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.

### Author(s)

Fabian Mueller

[Package RnBeads version 2.2.0 Index]