targetGstar {SHIP} | R Documentation |
Computation of the target Gstar.
Description
The p \times p
target Gstar is computed from the n \times
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 \bar{r}
in order to account
for negatively correlated genes within the same pathway
Usage
targetGstar(x, genegroups)
Arguments
x |
A |
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. |
Value
A p \times 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.
See Also
targetCor
, targetF
,
targetG
, targetGstar
, targetGpos
.
Examples
# 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 !