filter_mf_data: Filter molecular formula data by mass spectrometric metadata

In ume: Ultrahigh-Resolution Mass Spectrometry Data Evaluation for Complex Organic Matter

Filter molecular formula data by mass spectrometric metadata

Description

This function filters molecular formulas by isotope numbers, element ratios, etc.

Usage

filter_mf_data(
  mfd,
  c_iso_check = FALSE,
  n_iso_check = FALSE,
  s_iso_check = FALSE,
  ma_dev = 3,
  dbe_max = 999,
  dbe_o_min = -999,
  dbe_o_max = 999,
  mz_min = 1,
  mz_max = 9999,
  n_min = 0,
  n_max = 999,
  s_min = 0,
  s_max = 999,
  p_min = 0,
  p_max = 999,
  oc_min = 0,
  oc_max = 999,
  hc_min = 0,
  hc_max = 999,
  nc_min = 0,
  nc_max = 99,
  verbose = FALSE,
  ...
)

Arguments

mfd	data.table with molecular formula data as derived from ume::assign_formulas. Column names of elements/isotopes must match names in the isotope column of ume::masses; values are integers representing counts per formula.
c_iso_check	(TRUE / FALSE); check if formulas are verified by the presence of the main daughter isotope
n_iso_check	(TRUE / FALSE); check if formulas are verified by the presence of the main daughter isotope
s_iso_check	(TRUE / FALSE); check if formulas are verified by the presence of the main daughter isotope
ma_dev	Deviation range of mass accuracy in +/- ppm (default: 3 ppm)
dbe_max	Maximum number for DBE
dbe_o_min	Minimum number for DBE minus O atoms
dbe_o_max	Maximum number for DBE minus O atoms
mz_min	Minimum of mass to charge value
mz_max	Maximum of mass to charge value
n_min	Minimum number of nitrogen atoms
n_max	Maximum number of nitrogen atoms
s_min	Minimum number of nitrogen atoms
s_max	Maximum number of nitrogen atoms
p_min	Minimum number of nitrogen atoms
p_max	Maximum number of nitrogen atoms
oc_min	Minimum atomic ratio of oxygen / carbon
oc_max	Maximum atomic ratio of oxygen / carbon
hc_min	Minimum atomic ratio of hydrogen / carbon
hc_max	Maximum atomic ratio of hydrogen / carbon
nc_min	Minimum atomic ratio of nitrogen / carbon
nc_max	Maximum atomic ratio of nitrogen / carbon
verbose	logical; if TRUE, show progress messages.
...	Additional arguments passed to methods.

Value

data.table; subset of original molecular formula table

Author(s)

Boris P. Koch

See Also

Other Formula subsetting: filter_int(), filter_mass_accuracy(), remove_blanks(), subset_known_mf(), ume_assign_formulas(), ume_filter_formulas()

Examples

filter_mf_data(mfd = mf_data_demo, dbe_o_max = 10)

ume documentation built on Dec. 13, 2025, 1:06 a.m.