Trie nearly finished

source/skeleton.R

@@ -352,24 +352,11 @@ SK_SS_tripartite <- function(GE, PK, SK, parts, I=1, debug=FALSE, alpha=0.05, be
   
   
   # Extract every partition's GE,PK,SK parts
-  GE_in <- list()
   PK_in <- list()
   SK_in <- list()
 
-  for(i in 1:length(parts))
+  for(i in 2:length(parts))
   {
-    # GE
-    subGE <- GE[, parts[[i]]]
-    subGE <- as.matrix(subGE)
-    colnames(subGE) <- parts[[i]]
-    GE_in[[i]] <- subGE
-    remove(subGE)
-    
-    # interactions are 1 less, e.g., for K parts there are K-1 interaction parts
-    if(i == 1){
-      next
-    }
-    
     # PK
     subPK <- PK[parts[[i-1]],parts[[i]]]
     subPK <- as.matrix(subPK)
@@ -410,7 +397,7 @@ SK_SS_tripartite <- function(GE, PK, SK, parts, I=1, debug=FALSE, alpha=0.05, be
 
   set.seed(0)
   
-  return(c_SK_SS(GE_in,PK_in,SK_in, sizes, param_in,
+  return(c_SK_SS(PK_in,SK_in, sizes, param_in,
                  I, debug, alpha, beta_L, beta_H,
                  score_G, score_change_G))
 }