targetG: Computation of target G ('knowledge-based constant...
In SHIP: SHrinkage covariance Incorporating Prior knowledge

Description Usage Arguments Value Author(s) References See Also Examples

The p x p target G is computed from the n x p data matrix. It is defined as follows (i,j = 1,...,p):

sii if i=j ; r√{s_{ii}s_{jj}} if i~j ; 0 otherwise

where r is the average of sample correlations and sij denotes the entry of the unbiased covariance matrix in row i, column j. The notation i ~ j means that genes i and j are connected, i.e. genes i and j are in the same gene functional group.

1	targetG(x, genegroups)

`x`	A n x 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.

Monika Jelizarow and Vincent Guillemot

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.

# A short example on a toy dataset
# require(SHIP)
data(expl)
attach(expl)
tar <- targetG(x,genegroups)
which(tar[upper.tri(tar)]!=0) # not many non zero coefficients !