R/deleteEntries.R

In kroemerlab/GRMeta: Processing MetX data

deleteEntries<-function(obj,...,verbose=TRUE){
  
  if(!inherits(obj, "metaboSet")) stop("This is not a metaboSet object")
  
  dots <- list(...)
#  print(dots)
  errMsg=paste("Use any of the following for \n","samples:",
               paste(c(names(obj$Meta),names(obj$File)),collapse=" "),"\n","analytes:",
               paste(names(obj$Annot),collapse=" "),"\n",sep="")
  
  
  if(length(dots)==0) stop(errMsg)
#  print(dots)
  for(argname in names(dots)){
    
    if(!argname%in%c(names(obj$Meta),names(obj$File),names(obj$Annot))){
      cat(argname,errMsg,sep=" ")
      next
    }
    
    what=dots[[argname]]
    if(argname%in%c(names(obj$File),names(obj$Meta))){
      if(argname%in%names(obj$Meta)) l2keep=which(!obj$Meta[,argname]%in%what)
      if(argname%in%names(obj$File)) l2keep=which(!obj$File[,argname]%in%what)
      if(length(l2keep)>0 & length(l2keep)<length(obj$Sid)){
        sidori=obj$Sid
        obj$Sid=obj$Sid[l2keep]
        obj$Meta=obj$Meta[l2keep,]
        obj$File=obj$File[l2keep,]
        obj$Data=lapply(obj$Data,function(x) x[l2keep,,drop=F])

        if(!is.null(obj[['Eic']]))  if(!is.null(obj[['Eic']]$Samp)) obj[['Eic']]$Samp=obj[['Eic']]$Samp[l2keep,]

        if(any(!sidori%in%obj$Sid)){
          if(verbose) cat("Samples removed based on",argname,":\n",sidori[!sidori%in%obj$Sid],"\n",sep=" ")
          if(!verbose) cat("Samples removed based on",argname,": ",length(sidori[!sidori%in%obj$Sid]),"\n",sep=" ")
        }
        if(any(what%in%obj$Sid)){
          if(verbose) cat("Samples not excluded based on",argname,":\n",what[what%in%obj$Sid],"\n",sep=" ")
          if(!verbose) cat("Samples not excluded based on",argname,": ",length(what[what%in%obj$Sid]),"\n",sep=" ")
        }
      }
    }
    
    if(argname%in%names(obj$Annot)){
      l2keep=which(!obj$Annot[,argname]%in%what)
      if(length(l2keep)>0 & length(l2keep)<nrow(obj$Annot)){
        anaori=obj$Analyte
        obj$Analyte=obj$Analyte[l2keep]
        obj$Annot=obj$Annot[l2keep,]
#         print(table(table(l2keep)))
        #         print(sapply(obj$Data,dim))
          #     print(max(l2keep))
#         print(sapply(obj$Data,dim))
#         print(l2keep)
#         for(ix in names(obj$Data)){
#           print(ix)
#           obj$Data=obj$Data[,l2keep,drop=F]
#         }
        obj$Data=lapply(obj$Data,function(x) x[,l2keep,drop=F])
        #print("OKK")
        
        if(!is.null(obj[['Eic']])) if(!is.null(obj[['Eic']]$File)) obj[['Eic']]$File=obj[['Eic']]$File[l2keep,]
        
        if(!is.null(obj[['EicDef']])) if(!is.null(obj[['EicDef']]$Analyte)) obj[['EicDef']]=obj[['EicDef']][obj[['EicDef']]$Analyte%in%obj$Analyte,]
        
        
        if(any(!anaori%in%obj$Analyte)){
          if(verbose) cat("Analytes removed based on ",argname,":\n",anaori[!anaori%in%obj$Analyte],"\n",sep=" ")
          if(!verbose) cat("Analytes removed based on ",argname,": ",length(anaori[!anaori%in%obj$Analyte]),"\n",sep=" ")
        }
        if(any(what%in%obj$Analyte)){
          if(verbose) cat("Analytes not excluded based on ",argname,":\n",what[what%in%obj$Analyte],"\n",sep=" ")
          if(!verbose) cat("Analytes not excluded based on ",argname,": ",length(what[what%in%obj$Analyte]),"\n",sep=" ")
        }
      }
    }
  }
  invisible(obj)
}