Extract Masses with mzR — tidy_mzR_extract_mzs • clamr

Open a specified file extract a compound of interest.

tidy_mzR_extract_mzs(
  tidy_mzR,
  clamr_config,
  mz_compounds,
  add_missing_scans = FALSE,
  plot_type = "none"
)

Arguments

tidy_mzR: output of tidy_mzR_from_msfile
clamr_config: a named list of mass spec parameters with special formatting of instrument tolerances generated by build_clamr_config.
mz_compounds: m/z(s) to query.
add_missing_scans: include scans with no signal as zeros in eic
plot_type: should a plot be generated; options are: none, print and return.

Value

a list containing:

eic - ion counts of mz_compounds in full scan data
fragmentation_events - meta information for MS2+ scans with mz_compounds as a precursorMz
fragmentation_data - masses and ic of MS2+ scans
summary_plot (optionally) - a summary plot will be added if plot_type = "return"