dna (version 2.1-2)

resultsModTest-class: Class "resultsModTest"

Description

Test whether the overall modular structure differs between the two networks.

Objects from the Class

Objects can be created by calls of the form new("resultsModTest", ...).

Slots

p.value:

Object of class "numeric" ~~

N:

Object of class "numeric" ~~

modules1:

Object of class "modules" ~~

modules2:

Object of class "modules" ~~

Methods

get.results

signature(object = "resultsModTest"): returns the p-value, test statistic, and the modules for each network for a test for overall modular structure.

summary

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.

show

signature(object = "resultsModTest"): summarizes the test for modular structure by summarizing the modules in each network and listing the test statistic and the p-value.

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 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 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)

# extract results for a test of modular structure
## Not run: results.tms=get.results(tms)
## Not run: results.tms
# }