mzR Compile/Install

apt-get update
apt-get install -y libnetcdf-dev
apt-get clean
source("https://bioconductor.org/biocLite.R")
biocLite("mzR")
wget --progress=dot:giga -O /results/E_coli_ion_trap.mzXML \
  http://cpm.lumc.nl/export/public_datasets/E_coli_ion_trap.mzXML
E_coli_ion_trap.mzXML
require(mzR)
# download E_coli_ion_trap.mzXML from http://cpm.lumc.nl/export/public_datasets/
aa <- openMSfile(E_coli_ion_trap.mzXML)
runInfo(aa) # should return metadata, scanCount = 32654 etc.
pl <- peaks(aa, 10000) # get peaklist from one spectrum
plot(pl, type='h', lwd=1, xlab='m/z', ylab='intensity') # plot spectrum
© 2018 Nextjournal GmbH