changes on double genedeletion

DESCRIPTION

@@ -2,7 +2,7 @@ Package: sybil
 Type: Package
 Title: Efficient Constrained Based Modelling in R
 Version: 1.3.4
-Date: 2015-11-16
+Date: 2015-04-18
 Authors@R: c(
 	     person(c("C.", "Jonathan"), "Fritzemeier", role = c("cre", "ctb"), email = "clausjonathan.fritzemeier@uni-duesseldorf.de"),
 	     person("Gabriel", "Gelius-Dietrich", role = c("aut")),

R/doubleGeneDel.R

@@ -195,20 +195,6 @@ doubleGeneDel <- function(model, geneList1, geneList2, lb = NULL, ub = NULL,
 
         # Exclude everything from tmpMAT we do not need.
         #tmpMAT <- tmpMAT[geneList1, geneList2, drop = FALSE]
-      
-    }
-    else {
-  
-        tmpMAT <- matrix(FALSE, nrow = num_genes, ncol = num_genes)
-        #diag(tmpMAT) <- TRUE
-        for (i in seq(along = geneList1)) {
-            tmpMAT[geneList1[i], geneList2[i]] <- TRUE
-        }
-    }
-
-    geneList11 <- geneList1
-    geneList22 <- geneList2
-    
 		geneList1 <- unique(geneList1)
 		geneList2 <- unique(geneList2)
 
@@ -221,18 +207,30 @@ doubleGeneDel <- function(model, geneList1, geneList2, lb = NULL, ub = NULL,
 
 		rownames(tmpMAT) <- geneList1
 		colnames(tmpMAT) <- geneList2
-    #print(tmpMAT)
-    #print(num_opt)  
+
+		deletions <- which(tmpMAT == TRUE, arr.ind = TRUE)
+
+		kogenesID <- cbind(geneList1[deletions[,"row"]],
+							geneList2[deletions[,"col"]])
+	}
+	else {
+
+#		tmpMAT <- matrix(FALSE, nrow = num_genes, ncol = num_genes)
+#		#diag(tmpMAT) <- TRUE
+#		for (i in seq(along = geneList1)) {
+#			tmpMAT[geneList1[i], geneList2[i]] <- TRUE
+#		}
+		
+		kogenesID <- cbind(geneList1, geneList2)
+		
+    }
 
 
 #------------------------------------------------------------------------------#
 #                               run optimization                               #
 #------------------------------------------------------------------------------#
 
-    deletions <- which(tmpMAT == TRUE, arr.ind = TRUE)
     
-    kogenesID <- cbind(geneList1[deletions[,"row"]],
-                       geneList2[deletions[,"col"]])
     kogenes   <- lapply(seq_len(nrow(kogenesID)), function(x) kogenesID[x, ])
 
     fd <- .generateFluxdels(model, kogenes)

inst/NEWS.Rd

@@ -6,6 +6,14 @@
 
 \newcommand{\CRANpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
 
+
+\section{Changes in version 1.3.4 2016-04-18}{
+  \itemize{
+    \item \code{doubleGeneDel} messed up the order of deletions when using exlicit gene lists.
+    \item corrected url of openCOBRA in the manual.
+  }
+}
+% ---------------------------------------------------------------------------- %
 \section{Changes in version 1.3.3 2015-11-25}{
   \itemize{
     \item \code{addReact} crashed for irreversible models.

man/sybil-package.Rd

@@ -64,7 +64,7 @@ model <- readTSVmod(prefix = "Ec_core",
   BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic
   reconstructions. \emph{BMC Bioinformatics} \bold{11}, 213.
 
-  The openCOBRA project \url{http://opencobra.sourceforge.net/}.
+  The openCOBRA project \url{https://opencobra.github.io/}.
 
   Becker, S. A., Feist, A. M., Mo, M. L., Hannum, G., Palsson, B. Ø.  and
   Herrgard, M. J. (2007) Quantitative prediction of cellular metabolism with