SHIP (version 2.0.3)

build.target: Creates a covariance target, optionally by using prior information (e.g. from KEGG pathways).

Description

The function `build.target()` is a wrapper function to build the various types of covariance targets: diagonal ("D"), constant correlation ("F"), knowledge based ("G", "Gpos", and "Gstar"), correlation ("cor").

Usage

build.target(x, genegroups = NULL, type = "D")

Value

A \(p \times p\) target covariance matrix of a certain type.

Arguments

x

An \(n \times p\) matrix.

genegroups

List of the groups each gene belongs to: each entry of the list is dedicated to a gene (identified the same way as in \(x\)). Each item of the list is thus a vector of pathway IDs. Default value = `NULL`.

type

Character string specifying the wished target: "D" (by default) for a diagonal target, "cor" for a correlation target, "G", "Gpos" and "Gstar" for a G-type target (see Jelizarow et al, 2010) and "F" for a F-target.

Author

Vincent Guillemot and Monika Jelizarow

References

M. Jelizarow, V. Guillemot, A. Tenenhaus, K. Strimmer, A.-L. Boulesteix, 2010. Over-optimism in bioinformatics: an illustration. Bioinformatics. Accepted.

See Also

targetCor, targetD, targetF, targetG, targetGpos, targetGstar,.

Examples

# Simulate dataset
x <- matrix(rnorm(20*30), 20, 30)
# Try different targets
build.target(x, type = "D")