diff --git a/mix.R b/mix.R index 29409ff9e49f53d1eae3da3e2aa275aa4c412f04..8d116043d8d143a34dc932ad8c90d515aa1e9515 100644 --- a/mix.R +++ b/mix.R @@ -81,7 +81,24 @@ rmbmix.single<-function(fn_data,stgs_alist,fn_cmpd_list,wd,mode,readMethod="mzR" w <-msmsRead(w,filetable=fn_table,readMethod="mzR",mode=mode) if (!dir.exists(archdir)) dir.create(archdir) fn_arch<-file.path(archdir,paste(fn_data,".archive",sep='')) - msmsWorkflow(w, mode=mode, steps=2:8,archivename=fn_arch) + w<-msmsWorkflow(w, mode=mode, steps=2:8,archivename=fn_arch) + mb<-newMbWorkspace(w) + mb<-resetInfolists(mb) + ## loadInfolists + ## addPeaks + bits<-strsplit(fn_data,split="\\.")[[1]] + fn_info<-if (length(bits)> 1) paste(head(bits,-1),collapse=".") else fn_data + infodir<-fn_info + fn_info<-paste(archdir,"/",fn_info,".csv",sep='') + mb<-mbWorkflow(mb,infolist_path=fn_info) + list(w=w,mb=mb) } -rmbmix<- Vectorize(rmbmix.single,vectorize.args=c("fn_data","stgs_alist")) + +rmbmix.mb2.single<-function(mb,infodir) { + mb <- resetInfolists(mb) + mb <- loadInfolists(mb,infodir) + mbWorkflow(mb) +} +rmbmix.mb2<-Vectorize(rmbmix.mb2.single,vectorize.args=c("mb","infodir"),SIMPLIFY=F) +rmbmix<- Vectorize(rmbmix.single,vectorize.args=c("fn_data","stgs_alist"),SIMPLIFY=F)