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

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/targetG.R

Description

The p x p target G is computed from the n x p data matrix. It is defined as follows (i,j = 1,...,p):

sii if i=j ; r√{s_{ii}s_{jj}} if i~j ; 0 otherwise

where r is the average of sample correlations and sij denotes the entry of the unbiased covariance matrix in row i, column j. The notation i ~ j means that genes i and j are connected, i.e. genes i and j are in the same gene functional group.

Usage

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targetG(x, genegroups)

Arguments

x

A n x 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 x p matrix.

Author(s)

Monika Jelizarow and Vincent Guillemot

References

See Also

targetCor, targetF, targetG, targetGstar, targetGpos.

Examples

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# 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 !

SHIP documentation built on May 29, 2017, 11:25 a.m.