ume_filter_formulas: Complete Formula subsetting / filtering (wrapper)

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

Complete Formula subsetting / filtering (wrapper)

Description

A wrapper function to filter molecular formulas according to a evaluation parameters.

Usage

ume_filter_formulas(mfd, 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.
verbose	logical; if TRUE, show progress messages.
...	Arguments passed on to filter_mf_data, subset_known_mf, calc_norm_int, filter_int, remove_blanks 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 select_category List of category names that should be selected exclude_category List of category names that should be ignored ms_id Character; name of the column identifying individual spectra (default: "file_id"). peak_id Character; name of the column identifying unique peaks (default: "peak_id"). peak_magnitude Character; name of the column containing peak intensity values (default: "i_magnitude"). normalization Character; normalization method to apply. One of "bp", "sum", "sum_ubiq", "sum_rank", "none". Default is "bp". n_rank Integer; number of top-ranked peaks to use for "sum_rank" normalization (default: 200). norm_int_min Lower threshold (>=) of (normalized) peak magnitude norm_int_max Upper threshold (<=) of (normalized) peak magnitude blank_file_ids Integer vector of file_id values that represent blank analyses. blank_prevalence Numeric between 0 and 1. Threshold for blank filtering: the proportion of blanks in which a molecular formula must occur before it is excluded from the sample data. For example, blank_prevalence = 0 (default) removes any formula detected in at least one blank, while blank_prevalence = 0.5 removes formulas detected in 50% or more of the blanks. ret_time_col Character scalar. Name of the retention-time column that contains the beginning of the retention time segment that corresponds to the mass spectrum. If NULL (default), the function will auto-detect the first column in c("ret_time_min","retention_time","rt","RT") that exists in mfd. If none is found, blanks are removed ignoring retention time.

Value

A data.table having molecular formula assignments for each mass. ume_filter_formulas(mfd = mf_data_demo, dbe_o_max = 15, norm_int_min = 2)

See Also

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

Other ume wrapper: ume_assign_formulas()

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