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README.org

+#+TITLE: RMassBank Compound Mix Workflow
+
+
+* Usage
+  The entire 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 ~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.