R/getTableAddressing.R

In MalathiSIDona/pathDESeq: Pathway-Based Differential Expression Analysis for RNA-Seq Data

#' Get the adjacency list addressing template. 
#'

#' Useful if you want to store the networks in their condensed upper-diagonal form while still

#' having the benefit of convenient addressing and/or if you are using a simulated dataset in

#' which you know the truth and want to store all the values in a single data.frame.
#'

#' Internal function used to get the addressing template for a data.frame to contain the adjacency 

#' list representation of a matrix.

#' @param variableNames the names of all genes to include in the adjacency list

#' @param truth The true adjacency matrix. Often will not be available, but is useful for 

#' debugging and testing.

#' @return A data.frame representing the adjacency list of the matrix provided.

#' @export
#' @author Jeffrey D. Allen \email{Jeffrey.Allen@@UTSouthwestern.edu}

#' @examples
#' 
#Load in the sample Protein-Protein-Interaction data that comes with this package.

#' data(PPI)
#' 

#' #Simulate a dataset based on the 44-gene topology provided.

#' sim <- simulateNetwork(net44)
#' 

#' 
#Convert the true, underlying adjacency list to an adjacency matrix

#' trueMat <- adj2mat(net44)
#' 
#' 
#Reconstruct using GeneNet

#' gn <- abs(buildGenenet(sim))

#' gn <- gn[upper.tri(gn)]
#'

#' wg <- abs(buildWgcna(sim))

#' wg <- wg[upper.tri(wg)]
#'

#' #Aggregate all results into a single data.frame

#' data <- getTableAddressing(rownames(sim), trueMat)

#' data <- cbind(data, gn, wg)
#' 

getTableAddressing <- function (variableNames, truth) {
  joint <- matrix(0, nrow = length(variableNames), ncol = length(variableNames))
  rownames(joint) <- variableNames
  colnames(joint) <- variableNames
  address <- cbind(row(joint)[upper.tri(joint)], col(joint)[upper.tri(joint)])
  address <- matrix(row.names(joint)[address], ncol = 2)
  upper <- upper.tri(joint)
  if (missing(truth)) {
    aggregate <- data.frame(address)
    colnames(aggregate) <- c("Source", "Dest")
  }
  else {
    aggregate <- data.frame(address, truth[upper])
    colnames(aggregate) <- c("Source", "Dest", "Truth")
  }
  return(aggregate)
}