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 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.

Author(s)

Monika Jelizarow and Vincent Guillemot

References

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 !


[Package SHIP version 2.0.3 Index]