targetCor: Computation of the target Cor.

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

View source: R/targetCor.R

Description

The p x p target Cor is computed from the n x 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 r is computed.

Usage

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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 x 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.

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 <- targetCor(x,genegroups)
which(tar[upper.tri(tar)]!=0) # not many non zero coefficients !

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