netresponse-package {netresponse} | R Documentation |
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 |
Leo Lahti, Olli-Pekka Huovilainen, Antonio Gusmao and Juuso Parkkinen. Maintainer: Leo Lahti leo.lahti@iki.fi
Leo Lahti et al.: Global modeling of transcriptional responses in interaction networks. Bioinformatics (2010). See citation('netresponse') for details.
# 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 )