build.target {SHIP} | R Documentation |
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")
Arguments
x |
An |
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 |
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. |
Value
A p \times p
target covariance matrix of a certain
type.
Author(s)
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")