Initial code for consense

R/consense.R

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+
+consense <- function(sN,minEdgeCC=length(sN),noLog = FALSE,silent = FALSE) {
+
+    #'Find consensus subnetworks
+    #'
+    #   sN: List of subnetworks resulting after edge removal and
+    #'@param sN List of subnetworks
+    #'@param minEdgeCC minimum number of subnetworks an edge appears in to be kept
+    #'@param noLog if FALSE, save process to an .Rdata log file
+    #'@param silent if FALSE, print process to console in real time
+    #'@return A list of consensus subnetworks as igraph objects
+
+    #INPUTS:
+    #   sN: List of subnetworks
+    #   minEdgeCC: minimum number of subnetworks an edge appears in to be kept#   method: method of edge removal
+    #   noLog: if FALSE, save process to an .Rdata log file#   delta: threshold for edge removal for given method
+    #   silent: if FALSE, print process to console in real time#   EGG: 'Heat Diffusion' annotated AGG, iGraph object.
+
+    #OUTPUT:
+    #   cSN: List of subnetworks resulting after edge removal and
+    #       subnetwork construction
+
+
+    #minEdgeCC = 0 #length(outputGraphs)
+    numGraphs <- length(outputGraphs)
+    sNEdges <- vector(mode="list", length=numGraphs)
+    sNVerts <- vector(mode="list", length=numGraphs)
+    edgePairsList <- c() #vector(mode="list", length=numGraphs)
+    for (i in 1:numGraphs){
+        print(i)
+        sNEdges <- igraph::as_data_frame(outputGraphs[[i]], what = "edges")
+        sNVerts <- igraph::as_data_frame(outputGraphs[[i]], what = "vertices")
+        # Find edgepairs
+        numEdges <- nrow(sNEdges)
+        print(sNEdges)
+        edgePairs <- character(length=numEdges) # * 2)
+        for (j in 1:numEdges){
+            print(edgePairs)
+            edgePairs[j] <- paste(sNEdges[j, 'from'], sNEdges[j, 'to'], sep='-')
+        }
+        edgePairsList <- c(edgePairsList, edgePairs)
+    }
+
+    # Weigh edges based on how many subnetworks they occur in
+    boolIndex <- as.vector(table(edgePairsList) >= minEdgeCC)
+    edgesToKeep <- edgePairsList[boolIndex]
+
+# Keep only edges with weight > minEdgeCC
+
+# Extract connected components
+
+   return(cSN)
+}