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UME 1.6.1

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@boriskoch boriskoch released this 10 May 08:55
v1.6.1
c39f118

Submitted to CRAN.

New features

  • calc_isotope_pattern() returns exact mass, nominal mass, probability,
    relative abundance, molecular formula (mf), and isotope-specific molecular
    formula (mf_iso) for each isotope peak.
  • inchi_to_mf(): Extracts molecular formula string from an InChI code.
  • check_neutral_mf(): Is a given string for a neutral molecular formula correct?
    • Added optional pre-validation of molecular formulas via check_neutral_mf() in convert_molecular_formula_to_data_table().
      Invalid, charged, or non-formula inputs now produce informative error messages.
    • Introduced robust parsing of molecular formulas based on masses,
      supporting a wide range of elements and isotope labels without hard-coded symbol lists.
  • calc_nm() and related workflows now correctly preserve input order and
    duplicate formulas when character vectors are supplied.

Stability and bug fixes

  • convert_molecular_formula_to_data_table()
    • Added new argument isotope_default. Unspecific element notation such as Mo can now be resolved either to the
      most abundant isotope ("most_abundant", default) or to the lightest isotope ("lightest").
    • Fixed parsing errors for formulas containing multi-letter element symbols (such as `Mg) that were previously misinterpreted.
    • Fixed incorrect splitting of multi-letter element symbols without counts (e.g. "Mo" was parsed as "M" + "o")
    • Resolved internal inconsistencies related to isotope handling and duplicate detection.
    • Fixed inconsistency where masses were calculated using the correct isotope but column names still reflected the lightest isotope
    • Original input order and duplicate molecular formulas are now preserved.
    • Improved handling of repeated element or isotope tokens such as C2H5OH or Cl3[37Cl2][37Cl4].
  • create_isotope_expanded_table() now also accepts character vectors of
    molecular formulas as input.
  • convert_data_table_to_molecular_formulas() was rewritten to preserve
    original row order and duplicate entries using internal row identifiers.
  • check_neutral_mf()
    • Fixed length mismatch in data.table assignment when handling non-empty entries
    • Improved robustness for inputs containing NA values

Improvements

  • uplot_ms()
    • Replaced .SD[order()]-based data reduction with a faster data.table::frank()-based ranking approach
    • Significantly improved performance for large peak lists (10⁵–10⁶+ peaks), especially when using data_reduction < 1
    • Reduced memory overhead by avoiding repeated sorting and subsetting operations
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