R/cleanMetaboNames.R

In tonedivad/GRMeta: Processing MetX data

cleanMetaboNames<-function(metnam,RegExpr=NULL,Syno=NULL){

  dictRegExpr<-dictSyno<-NULL
  if(any(is.na(RegExpr))){
    file=list.files(system.file(package = "GRMeta"),pattern = "dictRegExpr.rda$",full.names = TRUE)
  load(file)
  RegExpr=dictRegExpr
  rm('dictRegExpr')
  }
  
  if(any(is.na(Syno))){
    file=list.files(system.file(package = "GRMeta"),pattern = "dictSyno.rda$",full.names = TRUE)
    load(file)
    Syno=dictSyno
    rm('dictSyno')
  }
  
  vnam=metnam
  if(is.data.frame(RegExpr) & !is.null(RegExpr))  for(i in 1:nrow(RegExpr)) vnam=gsub(RegExpr$Before[i],RegExpr$After[i],vnam)
  if(is.data.frame(Syno) & !is.null(Syno)) for(i in 1:nrow(Syno)) vnam[which(vnam==Syno$Before[i])]=Syno$After[i]
  
  return(list(newnam=vnam,oldnams=metnam))
}


#  dictSyno=data.frame(Before=c("Dimethyl oxoglutaric acid","1-5.anhydroglucitol","Glyceraldehyde-3-phosphate" ,"Glyceraldehyde 3.phosphate", "Maltose Trehalose",
#                               "Dimethyl glycine","Di methyl glycine","Alpha tocopherol","Tocopherol","5-aminovaleric","Aminovaleric", "Phosphoenol pyruvate",
#                               "cytidine","adenosine","xanthosine","AMPc","AMP.10C13.5N15","COA", "ACETYLCOA POS", "ACETYLCOENZYME A.2C13", "malonyl coA"  ,  "SuccCoA"),
#                      After=c("Dimethyl-oxoglutaric acid","1,5-anhydroglucitol","Glyceraldehyde 3-phosphate", "Glyceraldehyde 3-phosphate" ,"Maltose;Trehalose" ,        
#                              "Dimethylglycine","Dimethylglycine","Alpha-tocopherol","Alpha-tocopherol","5-aminovaleric acid" , "5-aminovaleric acid","Phosphoenolpyruvic acid",
#                              "Cytidine","Adenosine","Xanthosine","cAMP","AMP_ISTD","CoA", "AcetylCoA", "AcetylCoA_ISTD", "MalonylCoA"  ,  "SuccinylCoA"  ),
#                      stringsAsFactors = FALSE)
#  save(file="dictSyno.rda",dictSyno)
#  dictRegExpr=data.frame(Before=c("__","_","^Beta\\.","^O\\.","^N\\.","^X([0-9]+)\\.","([A-Za-z])\\.([0-9])\\.([A-Za-z])","([A-Za-z])\\.([A-Za-z])","\\.$"," C13"),
#                         After=c(";"," ","Beta-","O-","N-","\\1-","\\1-\\2-\\3","\\1 \\2","","_ISTD"),stringsAsFactors = FALSE)
#  save(file="dictRegExpr.rda",dictRegExpr)



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