In jspaezp/msunfolderr:

knitr::opts_chunk$set(
  root.dir = tempdir(),  
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-",
  verbose = TRUE
)

msunfolderr

The goal of msunfolderr is to unfold mass spec raw files.

By that I Mean that there are tools designed to handle only MS1-MS2 data, so as a hacky solution one can generate a fake raw file containing only 2 levels of ms data to use the tool.

Example

This is a basic example which shows you how to solve a common problem:

require(msunfolderr)

# Initially we get the information on all the ms scans from the file.
# since the backend of this is the proteowizard sorftware tools, it SHOULD
# work with any vendor format just as well
datafile <- system.file("extdata", "081218-50fmolMix_180813173507.mzML", package = "msunfolderr")
spectable <- get_spectrum_table(datafile,
                                outdir = './tmp')
spectable

msfilters <- get_unique_filters(spectable)
msfilters # These are all the ms filters that are contained in the selected file

filtergroups <- get_filter_groups(msfilters, TRUE)
filtergroups # These would be the MS2-MS3 "pairs"

purrr::map2(names(filtergroups), filtergroups, function(x,y){
    outdir <- glue::glue('./tmp{x}', x = x)
    subset_ms(datafile,
              y,
              outdir)

    mzmlfiles <- dir(outdir, pattern = '.mzML', full.names = TRUE)
    for (file in mzmlfiles) {
        reducemslevels(file,
                       filepath.out = glue::glue(file, '_reduced.mzML'),
                       minmslevel = 1,
                       maxmslevel = 3,
                       reduction = 1)

    }
})

system2('ls','tmp*.*', stdout = TRUE)

jspaezp/msunfolderr documentation built on May 24, 2019, 12:36 a.m.