diff --git a/README.org b/README.org index acefe22a53860b4790ade1089e9f2f7220ada43e..24193007350b038670dedcdfc8335b98f180728b 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.