diff --git a/DESCRIPTION b/DESCRIPTION index 23483fd..64ea19c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: minval Type: Package Title: MINimal VALidation for Stoichiometric Reactions Version: 0.5 -Date: 2016-08-31 +Date: 2016-10-04 Author: Daniel Osorio [aut,cre], Janneth Gonzalez [aut], Andres Pinzon-Velasco [aut]. Maintainer: Daniel Osorio Suggests: diff --git a/vignettes/minval.Rmd b/vignettes/minval.Rmd deleted file mode 100644 index 930f435..0000000 --- a/vignettes/minval.Rmd +++ /dev/null @@ -1,73 +0,0 @@ ---- -title: "**MINVAL** - **MIN**imal **VAL**idation for Stoichiometric Reactions" -author: "Daniel Osorio, Janneth Gonzalez and Andres Pinzon-Velasco" -date: "`r Sys.Date()`" -output: - pdf_document: - toc: true - geometry: margin=1in ---- - -```{r setup, include=FALSE} -knitr::opts_chunk$set(echo = TRUE) -``` -# Introduction to MINVAL -The **MINVAL** package was designed as a tool to identify orphan metabolites and evaluate the mass and charge balance of stoichometric reactions. MINVAL also includes functions to write models in TSV and SBML formats, extract all reactants, products, metabolite names and compartments from a metabolic reconstruction. - -## Getting started -```{r message=FALSE} -library(minval) -library(sybilSBML) -``` -```{r} -glycolysis <- read.csv2(system.file("extdata", "glycolysisKEGG.csv", package = "minval")) -dim(glycolysis) -colnames(glycolysis) -```` -```{r} -head(glycolysis$REACTION) -``` -```{r} -valid <- isValidSyntax(glycolysis$REACTION) -valid -``` -```{r} -glycolysisValidated <- mapReactions(reactionList = valid, - referenceData = glycolysis, - by = "bool", - inverse = FALSE) -dim(glycolysisValidated) -``` -```{r message=FALSE} -convert2sbml(glycolysisValidated,"glycolysisValidated.xml") -glycoModel <- readSBMLmod("glycolysisValidated.xml") -glycoModel -optimizeProb(glycoModel) -``` -```{r} -chemicalData <- read.csv2(system.file("extdata", "chemData.csv", package = "minval")) -head(chemicalData) -``` -```{r} -balanced <- isBalanced(reactionList = glycolysisValidated$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 diff --git a/vignettes/minval.pdf b/vignettes/minval.pdf deleted file mode 100644 index 0c4e264..0000000 Binary files a/vignettes/minval.pdf and /dev/null differ