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

 Package: StarBioTrek

 Type: Package

 Title: StarBioTrek

-Version: 1.9.4

-Date: 04-15-2019

+Version: 1.9.5

+Date: 04-16-2019

 Author: Claudia Cava,

     Isabella Castiglioni

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

@@ -234,6 +234,14 @@ eucdistcrtlk <- function(dataFilt,pathway_exp){

 #heatmap(as.matrix(score_euc_dista_t),scale="column",margins =c(12,9))

+#listpathgenees<-GE_matrix(dataFilt,pathway_exp)

+#listpathgenees<-listpathgenees[!sapply(listpathgenees, is.null)]

+#listpathgenees<-lapply(listpathgenees,function(x) apply(x,2,sd))

+

+

+#listpathgenees<-listpathgenees[!sapply(listpathgenees, function(x) all(is.na(x)))]

+#gsmatrix_sd<-do.call("rbind",listpathgenees)

+

 #' @title For TCGA data get human pathway data and creates a measure of standard deviations among pathways 

 #' @description stdv creates a matrix with standard deviation for pathways  

@@ -255,9 +263,6 @@ stdv<-function(gslist){

-

-

-

 #' @title For TCGA data get human pathway data and creates a measure of discriminating score among pathways 

 #' @description dsscorecrtlk creates a matrix with  discriminating score for pathways  

 #' @param dataFilt TCGA matrix

@@ -269,6 +274,13 @@ stdv<-function(gslist){

 dsscorecrtlk<-function(dataFilt,pathway_exp){

   listpathgenees<-GE_matrix(dataFilt,pathway_exp)

   PEAmatrix<-average(listpathgenees)

+  

+  # standard deviation

+  PEAmatrix_sd<-stdv(listpathgenees)

+  r<-intersect(rownames(PEAmatrix),rownames(PEAmatrix_sd))

+  PEAmatrix<-PEAmatrix[r,]

+  PEAmatrix_sd<-PEAmatrix_sd[r,]

+  

   #step 5 distance

   # EUCLIDEA DISTANCE

   df=combn(rownames(PEAmatrix),2) # possibili relazioni tra i pathway

@@ -281,7 +293,7 @@ dsscorecrtlk<-function(dataFilt,pathway_exp){

     distance<-dist(patients) # calcolo distanza EUCLIDEA tra le possibile combinazioni

     ma_d[,p]<-distance

   }

-  PEAmatrix_sd<-stdv(listpathgenees)

+  

   df=combn(rownames(PEAmatrix_sd),2) 

   df=t(df)

   ma<-matrix(0,nrow(df),ncol(PEAmatrix_sd)) # creo matrix che conterr le somme delle dev st

@@ -300,8 +312,9 @@ dsscorecrtlk<-function(dataFilt,pathway_exp){

   for( i in 1: ncol(pp2)){

     pp2[,i] <- as.numeric(as.character(pp2[,i]))

-return(pp2)

-}

+

+  }

+  return(pp2)

 }