## Not run:
#
# ##################################################
# # (1) Define path to an LC-HRMS .mzML file (not provided with package):
#
# filepath.mzML<-"C:/.../2012_07_01.mzML"
#
# # (2) Initialize an MSlist object and load this .mzML file into it:
#
# MSlist<-readMSdata(filepath.mzML, MSlevel=c(1))
#
# # (3) Partition the measurements now available in MSlist:
#
# MSlist<-mzagglom(MSlist,dmzgap=10,ppm=TRUE,drtgap=500,minpeak=4,maxint=1E7)
#
# # (4) EIC clustering of the partitions now available in MSlist:
#
# MSlist<-mzclust(MSlist,dmzdens=5,ppm=TRUE,drtdens=120,minpeak=4)
#
# # (5) Peak picking within the EIC clusters now available in MSlist:
#
# MSlist<-mzpick(MSlist, minpeak = 4, drtsmall = 50, drtfill = 10, drttotal = 200, recurs = 4,
# weight = 2, SB = 3, SN=2, minint = 1E4, maxint = 1e+07, ended = 2)
#
# # (6) Export a peak list now available in MSlist:
#
# writePeaklist(MSlist,"directory","filename")
#
# # (7) View your partitioning / EIC clustering / peak picking results:
#
# plotMSlist(MSlist,ppmbar=10);
# ##################################################
#
# ##################################################
# # Do above steps (1) to (5) in one wrap, then export a peak list:
#
# MSlist<-enviPickwrap( filepath.mzML,
# MSlevel=c(1),
# dmzgap=10,
# dmzdens=5,
# ppm=TRUE,
# drtgap=1000,
# drtsmall=20,
# drtdens=250,
# drtfill=10,
# drttotal=200,
# minpeak=4,
# recurs=10,
# weight=2,
# SB=3,
# SN=2,
# minint=10E4,
# maxint=10E6,
# ended=2,
# progbar=TRUE
# )
#
# writePeaklist(MSlist,"directory","filename")
# ##################################################
#
# ## End(Not run)
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