Description Methods References Examples
summary-methods
signature(x = "modules")
summarizes a network by listing the number of genes in each module.
signature(x = "resultsIndTest")
summarizes the tests for differential connectivity of individual genes by listing the number of genes which are significant at various significance levels.
signature(x = "resultsModTest")
summarizes the test for modular structure by summarizing the modules in each network and listing the test statistic and the p-value.
Gill, R., Datta, S., and Datta, S. (2010) A statistical framework for differential network analysis from microarray data. BMC Bioinformatics, 11, 95.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | # artificial example to show how to obtain a summary of the modules from a
# matrix of connectivity scores
set.seed(26)
s=matrix(runif(100,-1,1),10,10);diag(s)=1;s=round((s+t(s))/2,1)
the.modules=network.modules(s,m=3,epsilon=.7)
summary(the.modules)
# small example illustrating test procedures
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))
colnames(X1)=paste("G",1:6,sep="")
X2=rbind(
c(4.5,2.4,6.8,5.6,4.5,1.2,4.5),
c(7.6,9.0,0.1,3.4,5.6,5.5,1.2),
c(8.3,4.5,7.0,1.2,4.3,3.7,6.8),
c(3.4,1.1,6.9,7.2,3.1,0.9,6.6),
c(3.4,2.2,1.3,5.5,9.8,6.7,0.6))
colnames(X2)=paste("G",8:2,sep="")
# perform a test for differential connectivity of individual genes
# with PLS connectivity scores and squared distances
## Not run: tig=test.individual.genes(X1,X2)
## Not run: summary(tig)
# perform a test for modular structure using a minimum module size of 2
# and threshold of .5 with PLS connectivity scores
## Not run: test.modular.structure(X1,X2,min.module.size=2)
## Not run: summary(tms)
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