R/extractGeneAssociations.R

In BiGGR: Constraint based modeling in R using metabolic reconstruction databases

##extract gene information from database
extractGeneAssociations <- function(database){
lapply(database@model@reactions, function(r){
gene.ass <- NA
if (length(r@notes)>0){
  gene.ass <- gsub(".*GENE.ASSOCIATION:(.*?)</.*>.*$", "\\1", r@notes)
  gene.ass <- ifelse(gene.ass==r@notes, NA, gene.ass)
}
gene.ass
})
}