netresponse (version 1.32.2)

netresponse-package: NetResponse: Global modeling of transcriptional responses in interaction networks

Description

Global modeling of transcriptional responses in interaction networks. ll{ Package: netresponse Type: Package Version: See sessionInfo() or DESCRIPTION file Date: 2011-02-03 License: GNU GPL >=2 LazyLoad: yes }

References

Leo Lahti et al.: Global modeling of transcriptional responses in interaction networks. Bioinformatics (2010). See citation("netresponse") for details.

Examples

# Define parameters for toy data
Ns <- 200  # number of samples (conditions)
Nf <- 10   # number of features (nodes)
feature.names <- paste("feat", seq(Nf), sep="")
sample.names  <- paste("sample", seq(Ns), sep="") 
# random seed
set.seed( 123 )
# Random network
netw <- pmax(array(sign(rnorm(Nf^2)), dim = c(Nf, Nf)), 0)
# in pathway analysis nodes correspond to genes
rownames(netw) <- colnames(netw) <- feature.names
# Random responses of the nodes across conditions 
D <- array(rnorm(Ns*Nf), dim = c(Ns,Nf), dimnames = list(sample.names, feature.names))
D[1:100, 4:6]  <- t(sapply(1:(Ns/2),function(x){rnorm(3, mean = 1:3)}))
D[101:Ns, 4:6] <- t(sapply(1:(Ns/2),function(x){rnorm(3, mean = 7:9)}))
# Calculate the model
model <- detect.responses(D, netw)
# Subnets (each is a list of nodes)
get.subnets( model )

# Retrieve model for one subnetwork
# means, standard devations and weights for the components
inds <- which(sapply([e-mail], length) > 2)
subnet.id <- names(model@subnets)[[1]]
m <- get.model.parameters(model, subnet.id) 
print(m)