netresponse-package {netresponse} | R Documentation

## 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 leo.lahti@iki.fi

### 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(model@last.grouping, length) > 2)
    subnet.id <- names(model@subnets)[[1]]
    m <- get.model.parameters(model, subnet.id)
    print(m)

[Package netresponse version 1.40.0 Index]