From 4afadcb6140b01657c3c87902c0cd37bc8fafa35 Mon Sep 17 00:00:00 2001
From: Daniel Osorio <dcosorioh@unal.edu.co>
Date: Thu, 29 Sep 2016 11:50:30 -0500
Subject: [PATCH] Update MINVAL

---
 vignettes/minval.Rmd | 24 ++++++++++++++++++++++--
 1 file changed, 22 insertions(+), 2 deletions(-)

diff --git a/vignettes/minval.Rmd b/vignettes/minval.Rmd
index eb9f43e..930f435 100644
--- a/vignettes/minval.Rmd
+++ b/vignettes/minval.Rmd
@@ -18,8 +18,9 @@ knitr::opts_chunk$set(echo = TRUE)
 The **MINVAL** package was designed as a tool to identify orphan metabolites and evaluate the mass and charge balance of stoichometric reactions. MINVAL also includes functions to write models in TSV and SBML formats, extract all reactants, products, metabolite names and compartments from a metabolic reconstruction.
 
 ## Getting started
-```{r}
+```{r message=FALSE}
 library(minval)
+library(sybilSBML)
 ```
 ```{r}
 glycolysis <- read.csv2(system.file("extdata", "glycolysisKEGG.csv", package = "minval"))
@@ -42,7 +43,6 @@ dim(glycolysisValidated)
 ```
 ```{r message=FALSE}
 convert2sbml(glycolysisValidated,"glycolysisValidated.xml")
-library(sybilSBML)
 glycoModel <- readSBMLmod("glycolysisValidated.xml")
 glycoModel
 optimizeProb(glycoModel)
@@ -50,4 +50,24 @@ optimizeProb(glycoModel)
 ```{r}
 chemicalData <- read.csv2(system.file("extdata", "chemData.csv", package = "minval"))
 head(chemicalData)
+```
+```{r}
+balanced <- isBalanced(reactionList = glycolysisValidated$REACTION,
+                       referenceData = chemicalData,
+                       ids = "NAME",
+                       mFormula = "FORMULA")
+balanced
+```
+```{r}
+glycolysisBalanced <- mapReactions(reactionList = balanced,
+                                   referenceData = glycolysisValidated,
+                                   by = "bool",
+                                   inverse = FALSE)
+dim(glycolysisBalanced)
+```
+```{r message=FALSE}
+convert2sbml(glycolysisBalanced,"glycolysisBalanced.xml")
+glycoModel <- readSBMLmod("glycolysisBalanced.xml")
+glycoModel
+optimizeProb(glycoModel)
 ```
\ No newline at end of file