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Commit 5589185a authored by Todor Kondic's avatar Todor Kondic
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Update README.org

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......@@ -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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