RnBeads (version 1.4.0)

rnb.sample.groups: rnb.sample.groups

Description

Identifies sample subgroups defined in the given annotation information.

Usage

rnb.sample.groups(annotations, columns = NULL, columns.pairs = NULL, min.group.size = rnb.getOption("min.group.size"), max.group.count = rnb.getOption("max.group.count"))

Arguments

annotations

Methylation dataset as an object of type inheriting RnBSet, or its sample annotations in the form of a data.frame. If this parameter is a dataset, the annotation information is extracted using the method pheno.

columns

Optional; predefined column names (in the form of a character vector) or indices (an integer vector) to consider. All other columns in the annotation table will be ignored.

columns.pairs

Optional; a NAMED vector containing for each column name for which paired comparisons should be performed (say columnA) the name or index of another column (say columnB) in which same values indicate the same pairing. columnA should be the name of the value columnB in this vector.

min.group.size

Minimum number of samples in each subgroup. This must be a positive integer.

max.group.count

Maxumum number of subgroups defined by a trait. This must be an integer greater than 1.

Value

List of traits that define subgroups in the dataset. For each trait, the defined subgroups are represented by a list of integer vectors storing the corresponding sample indices.

Examples

library(RnBeads.hg19)
data(small.example.object)
str(rnb.sample.groups(rnb.set.example))