From 5589185ae3a3667f6e7c48557dd8f38ebd2a050e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Mon, 22 Jul 2019 11:19:06 +0200
Subject: [PATCH] Update README.org
---
README.org | 41 -----------------------------------------
1 file changed, 41 deletions(-)
diff --git a/README.org b/README.org
index acefe22..2419300 100644
--- a/README.org
+++ b/README.org
@@ -21,44 +21,3 @@
to be placed into the current working directory.
-
-** Record generation
- The entire sequentual procedure,
- #+BEGIN_SRC: R
- pos<-rmbmix::sw.do(list.files(patt=".*pos.mzML"),fn_cmpd_list="ChemistryDashboard-Batch-Search_2019-05-15_07_27_26.csv",mode="pH")
- pos_pmb<-rmbmix::mb.prep(pos)
- pos_mb<-rmbmix::mb.do(pos_pmb)
-
- neg<-rmbmix::sw.do(list.files(patt=".*neg.mzML"),fn_cmpd_list="ChemistryDashboard-Batch-Search_2019-05-15_07_27_26.csv",mode="mH")
- neg_pmb<-rmbmix::mb.prep(neg)
- neg_mb<-rmbmix::mb.do(neg_pmb)
-
- #+END_SRC
-
- The entire parallel procedure,
- #+BEGIN_SRC: R
- pos<-rmbmix::sw.do(list.files(patt=".*pos.mzML"),fn_cmpd_list="ChemistryDashboard-Batch-Search_2019-05-15_07_27_26.csv",mode="pH",proc=4)
- pos_pmb<-rmbmix::mb.prep(pos)
- pos_mb<-rmbmix::mb.do(pos_pmb,proc=4)
-
- neg<-rmbmix::sw.do(list.files(patt=".*neg.mzML"),fn_cmpd_list="ChemistryDashboard-Batch-Search_2019-05-15_07_27_26.csv",mode="mH",proc=4)
- neg_pmb<-rmbmix::mb.prep(neg)
- neg_mb<-rmbmix::mb.do(neg_pmb,proc=4)
-
- #+END_SRC
-
- The ~fn_cmpd_list~ argument is the compound list, from Chemistry
- Dashboard, or in a RMassBank format. The first argument to ~sw.do~ is
- the list of /mzML/ files containing spectral data to be processed
- using the spectral workflow. Each mzML file should have an associated
- /YAML/ file with RMassBank settings describing it. The settings file
- does not need to be complete, it can only contain the settings which
- are different from the settings template.
-
- Once the spectral workflow is complete, first run the MassBank
- preparation procedure using ~mb.prep~ function. Then, finalise the
- MassBank record workflow by using the ~mb.do~ function.
-
- The resulting record files and info lists are under
- "<data-dir>/info/XX" paths, where /data-dir/ is the mzML filename
- without the mzML suffix.
--
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