Computation of the target Cor.

The \(p \times p\) target Cor is computed from the \(n \times p\) data matrix. It it a modified version of target G. In particular, it tests the correlations (with a significance level of 0.05) and sets the non-significant correlations to zero before the mean correlation \(\bar{r}\) is computed.

Usage

targetCor(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.

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
tar <- targetCor(x,genegroups)
#> Error in targetCor(x, genegroups): could not find function "targetCor"
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'