hetset: Create 'hetset' Object

In ZytoHMGU/hetset: Identification of Heterogeneous Subsets in Data

Description

A data container is set up from data.frame, matrix or SummarizedExperiment object. Sample meta-data can be added.

Usage

hetset(D, S)

Arguments

D	data (rows contain features, samples in columns) in data.frame or matrix format.
S	data.frame (samples in rows) with supporting information about the samples. Needs do have "ID"-column for matching the samples in D.

Details

Creating a SummarizedExperiment data container with additional fields for storage of the mixture model fitted to the data.

Also a partitioning of the samples to the two subpopulations is included in the sample data (field prt).

Value

H is a SummarizedExperiment data container with additional (empty) fields for a two-component normal mixture fit. In the sample data, the field 'prt' is created, which will carry the assignment of each sample to one of the subpopulations. The metadata will get fields for the set of selected features, the default plotting method as well as the fitted parameters

prm.full	list(mean = ...) ...
prm.A	list ...
prm.B	list ...
prp.A	0.5

Author(s)

Daniel Samaga

References

Morgan M, Obenchain V, Hester J, Pagès H (2018). SummarizedExperiment: SummarizedExperiment container. R package version 1.12.0.

Examples

X <- matrix(data = rnorm(10*20),ncol = 50)
H <- hetset::hetset(D = X)

data("TCGA_HNSCC_expr")
Hds <- hetset(D = H)
summary(Hds)

ZytoHMGU/hetset documentation built on June 6, 2019, 2:16 p.m.