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SHIP (version 2.0.3)

targetG: Computation of target G ('knowledge-based constant correlation model').

Description

The \(p \times p\) target G is computed from the \(n \times p\) data matrix. It is defined as follows (\(i,j = 1,...,p\)): $$t_{ij} = \begin{cases} s_{ii} & \text{ if } i=j\\ \bar{r}\sqrt{s_{ii}s_{jj}} & \text{ if } i\neq j, i\sim j \end{cases}$$ where \(\bar{r}\) is the average of sample correlations and \(s_{ij}\) denotes the entry of the unbiased covariance matrix in row \(i\), column \(j\). The notation \(i\sim j\) means that genes \(i\) and \(j\) are connected, i.e. genes \(i\) and \(j\) are in the same gene functional group.

Usage

targetG(x, genegroups)

Value

A \(p \times p\) matrix.

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.

Author

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

Run this code

# 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 !

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