SHIP (version 1.0.2)

build.target: Creating a covariance target, optionally by using information from KEGG pathways.

Description

The function build.target() is a wrapper function to build the various types of covariance targets (D,F,G,Gpos,Gstar,cor).

Usage

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

Arguments

x

An $n x p$ 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.

type

Character string specifying the wished target: "D" 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.

Value

A $p x p$ target covariance matrix of a certain type.

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")