diff --git a/README.org b/README.org index 1df27f2f2027b6522dfda0524e7380bc47ee9df8..964bb466c032c81023c64471f31f8c7a14204ce2 100644 --- a/README.org +++ b/README.org @@ -2,30 +2,62 @@ * 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 +** Prescreening + 1. Generate prescreening data frames, + #+BEGIN_SRC R + presc.do(list.files(patt=".*mzML"),"pH",fn_cmpd_list="./Pesticides.info.csv",proc=4) + #+END_SRC + This is to be carried out inside the directory containing the + ~mzML~ files. For sequential execution, leave out the ~proc~ + argument. + 2. Plot, + #+BEGIN_SRC R + require(rmbmix) + presc.plot(normalizePath(list.dirs(".",recursive=F,full.names=F))) + #+END_SRC + The only argument is a sequence of absolute paths to directories + containing the prescreen data. The resulting plot file is going + 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) - 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. + #+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.