v1.1.3 pathRanker critical bugfix

Author: amfy10

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: NetPathMiner
-Version: 1.1.2
+Version: 1.1.3
 Date: 2014 onwards
 Title: NetPathMiner for Biological Network Construction, Path Mining
         and Visualization

R/netWeight.R

@@ -296,7 +296,7 @@ fetchAttribute <- function(graph, organism="Homo sapiens", target.attr, source.a
 #'                 missing.method = -1)
 #'  }
 #' 
-assignEdgeWeights <- function(microarray, graph, use.attr, y, weight.method="compCor", 
+assignEdgeWeights <- function(microarray, graph, use.attr, y, weight.method="cor", 
                                 complex.method="max", missing.method="median", same.gene.penalty ="median", 
                                 bootstrap = 100, verbose=TRUE) 
 {

src/PathRanker.cpp

@@ -172,7 +172,7 @@ st_shortest_path(const Vertex s, const Vertex t, Graph& g){
 
 pair<Graph,VertexPair> R_get_st_graph_from(SEXP nodes, SEXP edges,SEXP edge_weights);
 
-SEXP store_path_R(deque<Vertex>& st_path, Graph& g, double p_score);
+SEXP store_path_R(deque<Vertex> st_path, Graph& g, double p_score);
 
 SEXP pathranker(SEXP node_list, SEXP edge_list, SEXP edge_weights, SEXP rk,SEXP minpathsize)
 {
@@ -242,13 +242,14 @@ SEXP pathranker(SEXP node_list, SEXP edge_list, SEXP edge_weights, SEXP rk,SEXP
       break;
     }
 
+	/* disabled *****/
     // I want to make sure the path involves more than 1 gene
     // so the path distance must be greater than 2 times the s-> gene and gene->t
     // edges have the same weight.
     Edge e_temp = edge(p.sequence[0],p.sequence[1],g).first;
-    double fw = get(edge_weight, g)[e_temp];
+    //double fw = get(edge_weight, g)[e_temp];
 
-    if (p.sequence.size() > mps && p.score > 2*fw) {
+    if (p.sequence.size() > mps) {
       new_path = store_path_R(p.sequence,g,p.score);
       SET_VECTOR_ELT(all_paths,rsize,new_path);
       rsize = rsize + 1;
@@ -362,7 +363,7 @@ pair<Graph,VertexPair> R_get_st_graph_from(SEXP nodes, SEXP edges,SEXP edge_weig
   return ret;
 }
 
-SEXP store_path_R(deque<Vertex>& st_path, Graph& g, double p_score) {
+SEXP store_path_R(deque<Vertex> st_path, Graph& g, double p_score) {
   SEXP new_path,dimnames;
   SEXP genes,compounds,weights,distance;  
 

src/pathScope.cpp

@@ -693,7 +693,7 @@ extern "C" SEXP scope(SEXP node_list,
             for (it=reachedTargets.begin();it < reachedTargets.end();it++) {
                 if (last_compound.compare(*it) == 0) {
                     alreadyreached = 1;
-                    if (echo == 1) Rprintf(" - Already found a path to %s", last_compound.c_str());
+                    if (echo == 1) Rprintf(" - Already found a path to %s\n", last_compound.c_str());
                 }
             }
             if (alreadyreached == 0) {
@@ -702,9 +702,9 @@ extern "C" SEXP scope(SEXP node_list,
                     if (newpath != R_NilValue) {
                         SET_VECTOR_ELT(allpaths,vectid,newpath);   
                         reachedTargets.push_back(last_compound);
-                         if (echo == 1) Rprintf(" - Found a path to %s", last_compound.c_str());;
+                         if (echo == 1) Rprintf(" - Found a path to %s\n", last_compound.c_str());;
                     } else {
-                         if (echo == 1) Rprintf(" - Node out of scope");
+                         if (echo == 1) Rprintf(" - Node out of scope\n");
                     }
                 }
             }

vignettes/NPMVignette.Rnw

@@ -109,7 +109,6 @@ binaries suitable for your system from ``Download libSBML'' link. You can follow
 on the website.
 
 \subsubsection{Prerequisites for Windows users}
-#### Prerequisites for Windows users
 If you are installing the package through Bioconductor, you don't have to install external libraries. However, currently the Bioconductor version for Windows doesn't support SBML processing. Alternatively, we have prepared all dependencies in  a tar file, downloadable from \url{https://github.com/ahmohamed/NPM_dependencies} . Please download the file and place in in the home directory of R 
 (type "R RHOME" in command prompt to locate it).