Renamed function getReactionsList and improvements in gapFill and

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gibbslab · Dec 5, 2020 · e1e6746 · e1e6746
1 parent 7e9d120
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Showing 7 changed files with 11 additions and 8 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -4,7 +4,7 @@ Title: Find and Fill Gaps in Metabolic Networks
 Version: 0.3
 Authors@R: c(person("Kelly","Botero",role=c("aut")),
              person("Daniel","Osorio",email="[email protected]",role=c("aut","cre")),
-             person("Nicolas","Mendoza",role=c("aut")),
+             person("Nicolas","Mendoza-Mejia",role=c("aut")),
              person("Felipe","Rojas-Rodriguez",role=c("aut")),
              person("Janneth","Gonzalez",role=c("aut","ths")),
              person("Andres","Pinzon", role=c("aut","ths"))

diff --git a/NAMESPACE b/NAMESPACE
@@ -2,9 +2,9 @@
 
 export(additionCost)
 export(blockedReactions)
-export(extractModelReact)
 export(gapFill)
 export(gapFind)
+export(getReactionsList)
 export(getReference)
 importFrom("KEGGREST","keggGet")
 importFrom("KEGGREST","keggLink")

diff --git a/R/gapFill.R b/R/gapFill.R
@@ -44,6 +44,8 @@
 #' )
 #' }
 gapFill <- function(reactionList, reference, limit = 0.25, nRun = 5, woCompartment = FALSE, consensus = FALSE) {
+  reactionList <- gsub("->", "_>", reactionList)
+  reference <- gsub("->", "_>", reference)
   reference_reactants <- reactants(reference)
   reference_products <- products(reference)
   newR <- data.frame("addCost" = numeric(),"react" = character())

diff --git a/R/getReactionsList → R/getReactionsList.R b/R/getReactionsList → R/getReactionsList.R
diff --git a/R/getReference.R b/R/getReference.R
@@ -87,7 +87,6 @@ getReference <- function(organism = "all", sep = ";") {
       lines <- unlist(strsplit(b, "\n"))
       rx_obj <- lines[grepl("\\<reaction[[:space:]]+", lines)]
       if (length(rx_obj) > 0) {
-        message(b)
         rx_df <- do.call(rbind.data.frame, strsplit(rx_obj, '\"'))[, c(4, 6)]
         colnames(rx_df) <- c("rxn", "rev")
         return(rx_df)

diff --git a/README.md b/README.md
@@ -29,3 +29,5 @@ Available functions:
 Citation
 --------
 Kelly Botero, Daniel Osorio, Janneth Gonzalez and Andres Pinzon-Velasco (2016). **g2f: Find and Fill Gaps in Metabolic Networks**. R package version 0.1.
+
+Daniel Osorio, Andres Pinzon-Velasco, Nicolas Mendoza-Mejia, Felipe Rojas-Rodriguez and Janneth Gonzalez  (2020). **g2f as a Novel Tool to Find and Fill Gaps in Metabolic Networks**. R package version 0.1.
diff --git a/man/extractModelReact.Rd → man/getReactionsList.Rd b/man/extractModelReact.Rd → man/getReactionsList.Rd