@@ -1,8 +1,8 @@

 Package: StarBioTrek

 Type: Package

 Title: StarBioTrek

-Version: 1.0.2

-Date: 01-17-2017

+Version: 1.0.3

+Date: 02-09-2017

 Author: Claudia Cava,

     Isabella Castiglioni

 Maintainer: Claudia Cava <claudia.cava@ibfm.cnr.it>

@@ -15,7 +15,8 @@ Imports:

 	AnnotationDbi,

 	e1071,

 	ROCR,

-	grDevices

+	grDevices,

+	igraph

 Description: This tool StarBioTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data. 

 License: GPL (>= 3)

 biocViews: GeneRegulation,

@@ -27,4 +27,7 @@ importFrom(SpidermiR,SpidermiRquery_species)

 importFrom(e1071,svm)

 importFrom(e1071,tune)

 importFrom(grDevices,rainbow)

+importFrom(igraph,get.data.frame)

+importFrom(igraph,graph.data.frame)

+importFrom(igraph,induced.subgraph)

 importFrom(org.Hs.eg.db,org.Hs.egSYMBOL2EG)

@@ -522,32 +522,3 @@ list_pathkegg<-list(pathway.codes,b)

 return(list_pathkegg)

 }

-

-overlap <- function(net_type,x,currentPathway_genes){

-  de<-net_type[which(net_type$m_shar_pro==x),]

-  fr<-intersect(de$m2_shar_pro,currentPathway_genes)

-  go=list()

-  if(length(fr)!=0)    {

-    for (i in 1:length(fr)){

-      de2<-de[which(de$m2_shar_pro==fr[i]),]

-      go[[i]]<-de2

-    }

-  }            

-  dst<-do.call("rbind", go)

-  return(dst)

-}

-

-overlap_inv <- function(net_type,x,currentPathway_genes){

-  de<-net_type[which(net_type$m2_shar_pro==x),]

-  fr<-intersect(de$m_shar_pro,currentPathway_genes)

-  go=list()

-  if(length(fr)!=0)    {

-    for (i in 1:length(fr)){

-      de2<-de[which(de$m_shar_pro==fr[i]),]

-      go[[i]]<-de2

-    }

-  }            

-  dst<-do.call("rbind", go)

-  return(dst)

-}

-

@@ -1,54 +1,37 @@

 #' @title Get human KEGG pathway data and network data in order to define the common gene.

 #' @description path_net creates a list of network data for each human pathway. The network data will be generated when interacting genes belong to that pathway.  

-#' @param net_type  network data as provided by getNETdata

+#' @param data  network data as provided by getNETdata

 #' @param pathway  pathway data as provided by getKEGGdata

+#' @importFrom igraph graph.data.frame induced.subgraph get.data.frame

 #' @export

 #' @return a list of network data for each pathway (interacting genes belong to that pathway)

 #' @examples

-#' lista_net<-path_net(pathway=path,net_type=netw)

-path_net<-function(pathway,net_type){

+#' lista_net<-path_net(pathway=path,data=netw)

+path_net<-function(pathway,data){

   lista_int<-list()

-  colnames(net_type)<-c("m_shar_pro","m2_shar_pro")

   for (k in 1:ncol(pathway)){

-    #k=1 

-    print(paste(k,"PATHWAY",colnames(pathway)[k]))

+    print(colnames(pathway)[k])

     currentPathway_genes<-pathway[,k]

-    common1 <- intersect( net_type$m_shar_pro, currentPathway_genes)

-    common2 <- intersect( net_type$m2_shar_pro, currentPathway_genes)

-    if (length(common1)==0 & length(common2)==0 ){

-      mago2<-character(length = 0)

-    }

-    if (length(common1)!=0 | length(common2)!=0 ){

-      b=list()

-      for (i in 1:length(common1)){

-        x<-common1[i]

-        n<-overlap(net_type,x,currentPathway_genes)

-        b[[i]]<-n

-      }

-      v<-do.call("rbind", b)

-      c=list()

-      for (i in 1:length(common2)){

-        x<-common2[i]

-        n<-overlap_inv(net_type,x,currentPathway_genes)

-        c[[i]]<-n

-      }

-      v2<-do.call("rbind", c)

-      mago<-rbind(v,v2)

-      mago2<-mago[!duplicated(mago), ]

-    }

-    

-    if (length(mago2)!=0){

-      lista_int[[k]]<-mago2

-    }

-    if (length(mago2)==0){

-      lista_int[[k]]<-"0"} 

-    

+    colnames(data) <- c("gene_symbolA", "gene_symbolB")

+    i <- sapply(data, is.factor)

+    data[i] <- lapply(data[i], as.character)

+    ver<-unlist(data)

+    n<-unique(ver)

+    s<-intersect(n,currentPathway_genes)

+    g <- graph.data.frame(data,directed=FALSE)

+    g2 <- induced.subgraph(graph=g,vids=s)

+    aaa<-get.data.frame(g2)

+    colnames(aaa)[1] <- 'V1'

+    colnames(aaa)[2] <- 'V2'

+    lista_int[[k]]<-aaa

     names(lista_int)[k]<-colnames(pathway)[k] 

-  }   

+  }

   return(lista_int)

 }

+

+

 #' @title Get human KEGG pathway data and output of path_net in order to define the common genes.

 #' @description list_path_net creates a list of interacting genes for each human pathway.   

 #' @param lista_net  output of path_net

@@ -56,7 +39,7 @@ path_net<-function(pathway,net_type){

 #' @export

 #' @return a list of genes for each pathway (interacting genes belong to that pathway)

 #' @examples

-#' lista_netw<-path_net(pathway=path,net_type=netw)

+#' lista_netw<-path_net(pathway=path,data=netw)

 #' list_path<-list_path_net(lista_net=lista_netw,pathway=path)

 list_path_net<-function(lista_net,pathway){

 v=list()

@@ -65,6 +48,7 @@ for (j in 1:length(lista_net)){

   cf<-lista_net[[j]]

   i <- sapply(cf, is.factor) 

   cf[i] <- lapply(cf[i], as.character)

+  colnames(cf) <- c("m_shar_pro", "m2_shar_pro")

   m<-c(cf$m_shar_pro)

   m2<-c(cf$m2_shar_pro)

   s<-c(m,m2)

@@ -18,7 +18,7 @@ a list of genes for each pathway (interacting genes belong to that pathway)

 list_path_net creates a list of interacting genes for each human pathway.

 }

 \examples{

-lista_netw<-path_net(pathway=path,net_type=netw)

+lista_netw<-path_net(pathway=path,data=netw)

 list_path<-list_path_net(lista_net=lista_netw,pathway=path)

 }

@@ -4,12 +4,12 @@

 \alias{path_net}

 \title{Get human KEGG pathway data and network data in order to define the common gene.}

 \usage{

-path_net(pathway, net_type)

+path_net(pathway, data)

 }

 \arguments{

 \item{pathway}{pathway data as provided by getKEGGdata}

-\item{net_type}{network data as provided by getNETdata}

+\item{data}{network data as provided by getNETdata}

 }

 \value{

 a list of network data for each pathway (interacting genes belong to that pathway)

@@ -18,6 +18,6 @@ a list of network data for each pathway (interacting genes belong to that pathwa

 path_net creates a list of network data for each human pathway. The network data will be generated when interacting genes belong to that pathway.

 }

 \examples{

-lista_net<-path_net(pathway=path,net_type=netw)

+lista_net<-path_net(pathway=path,data=netw)

 }

@@ -463,7 +463,7 @@ The function `path_net` creates a network of interacting genes for each pathway.

 The output will be a network of genes belonging to the same pathway.  

 ```{r, eval = TRUE}

-network_path<-path_net(pathway=path,net_type=netw)

+network_path<-path_net(pathway=path,data=netw)

 ```