rnb.step.betadistribution: rnb.step.betadistribution
In RnBeads: RnBeads

Description Usage Arguments Value Details Author(s)

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

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

`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

The modified report.

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.

Fabian Mueller

RnBeads documentation built on March 3, 2021, 2 a.m.