as_peaklist: Check format of peaklist

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

Check format of peaklist

Description

Flexible entry point for UME. Accepts:

• data.frame / data.table peaklists

• numeric m/z vectors

• file paths (csv, txt, tsv, rds)

Normalizes column names, adds missing structural columns (file_id, peak_id), removes invalid rows, validates schema, and assigns the UME peaklist class. Creates a standardized data.table ready for formula assignment.

Usage

as_peaklist(pl, verbose = FALSE, track_original_names = TRUE, ...)

Arguments

pl	Input object representing a peaklist. Can be: data.frame or data.table file path to a supported tabular format numeric vector of m/z values
verbose	logical; if TRUE, show progress messages.
track_original_names	Logical (default: TRUE). If TRUE, as_peaklist() stores a "original_colnames" attribute mapping canonical UME names (e.g. "mz") to the user’s original column names (e.g. "m/z"). Internal functions that perform many ⁠:=⁠ operations (e.g. assign_formulas()) may set this to FALSE to avoid attribute- related shallow-copy warnings.
...	Reserved for future extensions.

Value

A validated and normalized peaklist as a data.table with class "ume_peaklist".

See Also

Other check ume objects: check_formula_library(), check_mfd()

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