R/model.stats.R

In antagomir/netresponse: Functional Network Analysis

#' @title model.stats
#' @description Subnetwork statistics: size and number of distinct responses for each subnet.
#' @param models NetResponse object or list of models
#' @return
#' A 'subnetworks x properties' data frame containing the following elements.
#' \item{subnet.size: }{ Vector of subnetwork sizes. } \item{subnet.responses:
#' }{ Vector giving the number of responses in each subnetwork. }
#' @author 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 reference details.
#' @keywords utilities
#' @export
#' @examples
#' # Load a pre-calculated netresponse model obtained with 
#' # model <- detect.responses(toydata$emat, toydata$netw, verbose = FALSE)
#' data(toydata)        
#' # Calculate summary statistics for the model
#' stat <- model.stats(toydata$model)
#' 
#' 
model.stats <- function(models) {
    
    # Check statistics for subnetworks subnetwork size number of responses
    
    if (is(models) == "NetResponseModel") {
        models <- models@models
    }
    
    if (is.null(names(models))) {
        names(models) <- seq_len(length(models))
    }
    
    Ncomps <- c()
    for (subnet.id in names(models)) {
        Ncomps[[subnet.id]] <- ncol(models[[subnet.id]]$qofz)
    }
    
    tab <- cbind(sapply(models, function(x) {
        ncol(x$mu)
    }), Ncomps)
    colnames(tab) <- c("nodes", "responses")
    rownames(tab) <- names(models)
    
    as.data.frame(tab)
    
}