diff --git a/R/mix.R b/R/mix.R index c34246fc58493576bce79975eb92a659b32a10cc..3825089b0df8728b2f76583c9c88f91256325f87 100644 --- a/R/mix.R +++ b/R/mix.R @@ -318,22 +318,16 @@ v<-function(fn_data,stgs_alist,wd,fn_cmpd_list,mode,readMethod="mzR",archdir="ar ##' @return result of RMB_EIC_Prescreen ##' @author Todor Kondić presc.single <- function(fn_data,stgs_alist,wd,mode,fn_cmpd_l,ppm_lim_fine=10,EIC_limit=0.001,nm_arch="archive") { - ## Generate settings file and load. - wd <- normalizePath(wd) - fn_data <- normalizePath(fn_data) - stgs_alist<-if (is.character(stgs_alist)) yaml::yaml.load_file(stgs_alist) else stgs_alist - sfn<-file.path(wd,paste(basename(fn_data),".ini",sep='')) - mk_sett_file(stgs_alist,sfn) - RMassBank::loadRmbSettings(sfn) + gen_stgs_and_load(fn_data,stgs_alist,wd) ## Generate and load the compound list. - fn_comp<-file.path(wd,paste(basename(fn_data),".comp.csv",sep='')) - n_cmpd<-gen_comp_list(fn_cmpd_l,fn_comp) + x <- gen_cmpdl_and_load(fn_data,wd,fn_cmpd_l) + fn_comp <- x$fn_cmpdl + n_cmpd <- x$n ## Generate file table. - df_table<-data.frame(Files=rep(fn_data,n_cmpd),ID=1:n_cmpd) - fn_table<-file.path(wd,paste("fn-table.",basename(fn_data),".csv",sep='')) - write.csv(x=df_table,file=fn_table,row.names=F) + gen_file_table(fn_data,n_cmpd,wd) + curd <- setwd(wd) res <- ReSOLUTION::RMB_EIC_prescreen(archive_name=nm_arch,RMB_mode=mode, FileList=fn_table,