netresponse-package: NetResponse: Global modeling of transcriptional responses in...

In antagomir/netresponse: Functional Network Analysis

NetResponse: Global modeling of transcriptional responses in interaction networks

Description

Global modeling of transcriptional responses in interaction networks.

Package:	netresponse
Type:	Package
Version:	See sessionInfo() or DESCRIPTION file
Date:	2011-02-03
License:	GNU GPL >=2
LazyLoad:	yes

Author(s)

Leo Lahti, Olli-Pekka Huovilainen, Antonio Gusmao and Juuso Parkkinen. Maintainer: Leo Lahti [e-mail]

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 )

antagomir/netresponse documentation built on March 30, 2023, 7:24 a.m.