diff --git a/README.org b/README.org new file mode 100644 index 0000000000000000000000000000000000000000..1df27f2f2027b6522dfda0524e7380bc47ee9df8 --- /dev/null +++ b/README.org @@ -0,0 +1,31 @@ +#+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.