remove_blanks: Remove molecular formulas detected in blanks

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

Remove molecular formulas detected in blanks

Description

Remove all molecular formulas that were detected in one or more blank analyses (identified via blank_file_ids). Matching is always on mf. If a retention-time column is present (or provided using ret_time_col), removal is restricted to the corresponding LC segment.

Usage

remove_blanks(
  mfd,
  blank_file_ids = NULL,
  blank_prevalence = 0.5,
  ret_time_col = NULL,
  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.
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.
verbose	logical; if TRUE, show progress messages.
...	Additional arguments passed to methods.

Details

• Requires a unique integer file_id per analysis in mfd.

• Minimal required columns in mfd: mf, file_id.

• Optional column: a retention-time column (e.g. "ret_time_min").

• If a retention-time column is used, formulas present in blanks are only removed for rows whose mf and retention time match

• The input mfd is not modified by reference; a subset is returned.

Value

data.table; subset of the original molecular formula table (mfd) with blank formulas removed (globally or LC-segment-wise).

Backward compatibility

The argument LCMS is deprecated and no longer used. Retention-time-aware removal is now enabled automatically when a retention-time column is present or explicitly provided via ret_time_col.

Author(s)

Boris P. Koch

See Also

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

Examples

# Presence/absence removal, no retention time:
remove_blanks(mfd = mf_data_demo,
              remove_blank_list = "Blank",
              verbose = TRUE)

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