RMassBank Compound Mix Workflow
Usage
Prescreening
- Generate prescreening data frames,
presc.do(list.files(path="~/ECI_SCRATCH/20190627_HEROBER",patt=".*.mzML",full.names=T), mode="pH",fn_cmpd_l="./cutlist.csv",proc=F,dest=".")
This is to be carried out inside the directory containing the
mzML
files. For sequential execution, leave out theproc
argument. - Plot,
require(rmbmix) presc.plot(list.files(".",patt="2.*POS",include.dirs=T),cex=0.7,digits=4)
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,
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 entire parallel procedure,
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)
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.