Computation of the target Gstar.

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 \(n \times p\) 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.

Value

A \(p \times p\) matrix.

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.

Author

Monika Jelizarow and Vincent Guillemot

Examples

# A short example on a toy dataset
# require(SHIP)
data(expl)
attach(expl)
#> The following objects are masked from expl (pos = 3):
#> 
#>     genegroups, x
#> The following objects are masked from expl (pos = 4):
#> 
#>     genegroups, x
#> The following objects are masked from expl (pos = 5):
#> 
#>     genegroups, x
#> The following objects are masked from expl (pos = 6):
#> 
#>     genegroups, x
#> The following objects are masked from expl (pos = 7):
#> 
#>     genegroups, x
tar <- targetGstar(x,genegroups)
#> Error in targetGstar(x, genegroups): could not find function "targetGstar"
which(tar[upper.tri(tar)]!=0) # not many non zero coefficients !
#> Error in as.vector(x, mode): cannot coerce type 'closure' to vector of type 'any'