From 06c7e8c4dab73aa85e67ee38ccd6bdba42539ec8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Fri, 21 Jun 2019 20:55:25 +0200
Subject: [PATCH] Update mix.R
* R/mix.R(presc.single): Update.
---
R/mix.R | 18 ++++++------------
1 file changed, 6 insertions(+), 12 deletions(-)
diff --git a/R/mix.R b/R/mix.R
index c34246f..3825089 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,
--
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