dna (version 2.1-2)

cornet: Correlation network

Description

Computes the connectivity scores for a network based on correlation.

Usage

cornet(data,rescale.scores=FALSE)

Arguments

data

microarray dataset with genes in columns and samples in rows.

rescale.scores

indicates whether PLS scores should be rescaled so that the largest score for each gene should be 1 in magnitude.

Value

cornet

a correlation matrix measuring the interactions between gene pairs.

References

Gill, R., Datta, S., and Datta, S. (2010) A statistical framework for differential network analysis from microarray data. BMC Bioinformatics, 11, 95.

Examples

# NOT RUN {
# small example using cornet without rescaled scores
X1=rbind(
c(2.5,6.7,4.5,2.3,8.4,3.1),
c(1.2,0.7,4.0,9.1,6.6,7.1),
c(4.3,-1.2,7.5,3.8,1.0,9.3),
c(9.5,7.6,5.4,2.3,1.1,0.2))
s=cornet(X1)
print(round(s,4))

# small example using cornet with rescaled scores
s2=cornet(X1,rescale.scores=TRUE)
print(round(s2,4))
# }