# targetGstar: Computation of the target Gstar. In SHIP: SHrinkage covariance Incorporating Prior knowledge

## Description

The p x p target Gstar is computed from the n x p data matrix. It it a modified version of target G. In particular, it involves two parameters for the correlation (a positive and a negative one) instead of the single parameter r in order to account for negatively correlated genes within the same pathway

## Usage

 1 targetGstar(x, genegroups) 

## Arguments

 x A n \times p data matrix. genegroups A list of genes obtained using the database KEGG, where each entry itself is a list of pathway names this genes belongs to. If a gene does not belong to any gene functional group, the entry is NA.

A p x p matrix.

## Author(s)

Monika Jelizarow and Vincent Guillemot

## References

• J. Schaefer and K. Strimmer, 2005. A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Statist. Appl. Genet. Mol. Biol. 4:32.

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

targetCor, targetF, targetG, targetGstar, targetGpos.
 1 2 3 4 5 6 # A short example on a toy dataset # require(SHIP) data(expl) attach(expl) tar <- targetGstar(x,genegroups) which(tar[upper.tri(tar)]!=0) # not many non zero coefficients !