targetG {SHIP} | R Documentation |
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)
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 <- targetG(x,genegroups)
which(tar[upper.tri(tar)]!=0) # not many non zero coefficients !