R/buildConsensus.R

In blogsdon/metanetwork: Network meta analysis

#' This function builds the Consensus Network from the component network
#' 
#' This function builds a consensus co-expression network.
#' 
#' @param outputpath Required. Local directory to load files from and save files to. 
#' @param networkFolderId Required. The Synapse parent ID of the folder containing
#' the folders with the individual networks.
#' @param fileName Required. The input file path.
#' @param bar Required. File paths object with network paths 
#' @param iscsv Optional. Is the data matrix a csv file. If not assumes it is tab delimited. (Default = TRUE).
#' @inheritParams synGetFiles
#' 
#' @export 
#' @return Saves a rankc consensus network to `outputpath` and saves the BICNetwork
#'  object to `outputpath` if `fileName` is specified
#' 
buildConsensus = function(outputpath, networkFolderId, fileName, pattern_id, bar, iscsv = TRUE){
  
  #get all networks from Synapse
  #bar <- synGetFiles(networkFolderId, downloadLocation = outputpath, pattern_id = pattern_id)
  
  loadNetwork <- function(file){
    sparrowNetwork <- data.table::fread(file,stringsAsFactors=FALSE,data.table=F)
    rownames(sparrowNetwork) <- sparrowNetwork$V1
    sparrowNetwork <- sparrowNetwork[,-1]
    gc()
    return(sparrowNetwork)
  }
  getPaths <- function(bar){
    names <- c()
    for (i in 1:length(bar)){
      temp <- bar[[i]]$path
      names <- append(names,temp)
    }
    return(names)
  }
  
  networkFiles <- getPaths(bar)
  networks <- lapply(networkFiles,loadNetwork)
  networks <- lapply(networks,data.matrix)
  
  networks$rankConsensus <- metanetwork::rankConsensus(networks)
  cat('built rank consensus\n')
  cat('write rank consensus\n')
  utils::write.csv(networks$rankConsensus,file=paste0(outputpath,'rankConsensusNetwork.csv'),quote=F)
    #library(Matrix)
   getNetmethod <- function(networkname){
     temp_names <- strsplit(strsplit(networkname,'Network.csv')[[1]][1],'_')[[1]]
     temp_names <- unlist(temp_names[length(temp_names)])
     return(temp_names)
   }
   networkMethods <- sapply(networkFiles,getNetmethod)
   cat('grabbed methods\n')
   #build rank consensus
   cat('updated methods\n')
   networkMethods <- c(networkMethods,'rankConsensus')
   cat('reading in data\n')
   options(stringsAsFactors = F)
   # load Dataset
   cat('turning data into data matrix\n')
   if( isTRUE(iscsv) ){
    dataSet <- readr::read_csv(fileName, row.names=1)
   }else{ 
    dataSet <- data.table::fread(fileName) %>% as.matrix(rownames=1)
   }
   #-#dataSet <- data.matrix(dataSet)
   dataSet <- t(dataSet)
   cat('build bicNetworks\n')
   #bicNetworks <- lapply(networks,metanetwork::computeBICcurve,dataSet,maxEdges=1e5)
   bicNetworks <- metanetwork::computeBICcurve(networks$rankConsensus,dataSet,maxEdges=2e5)
   #cat('make names of bicNetworks\n')
   #names(bicNetworks) <- 'rankConsensus'
   cat('save bicNetworks\n')
   save(bicNetworks,file=paste0(outputpath,'bicNetworks.rda'))
}