as_peaklist

Flexible entry point for UME. Accepts:<ul>
<li>data.frame / data.table peaklists</li>
<li>numeric m/z vectors</li>
<li>file paths (csv, txt, tsv, rds)</li>
</ul>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 <code>data.table</code> ready for formula assignment.

Provides tools for assigning molecular formulas from exact masses
obtained by ultrahigh-resolution mass spectrometry. The methodology follows
the workflow described in Leefmann et al. (2019) <doi:10.1002/rcm.8315>.
The package supports the inspection, filtering and visualization of
molecular formula data and includes utilities for calculating common
molecular parameters (e.g., double bond equivalents, DBE). A graphical
user interface is available via the 'shiny'-based 'ume' application.

Boris Koch

Ultrahigh-Resolution Mass Spectrometry Data Evaluation for
Complex Organic Matter

as_peaklist function

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

Arguments

Flexible entry point for UME. Accepts:<ul>
<li>data.frame / data.table peaklists</li>
<li>numeric m/z vectors</li>
<li>file paths (csv, txt, tsv, rds)</li>
</ul>

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 <code>data.table</code> ready for formula assignment.

Check format of peaklist — as_peaklist

<dl>

<dt>pl</dt>
<dd>Input object representing a peaklist. Can be:<ul>
<li>data.frame or data.table</li>
<li>file path to a supported tabular format</li>
<li>numeric vector of m/z values</li>
</ul></dd>


<dt>verbose</dt>
<dd>logical; if <code>TRUE</code>, show progress messages.</dd>


<dt>track_original_names</dt>
<dd>Logical (default: TRUE). If TRUE,
<code>as_peaklist()</code> stores a <code>"original_colnames"</code> attribute mapping
canonical UME names (e.g. <code>"mz"</code>) to the user’s original column names
(e.g. <code>"m/z"</code>). Internal functions that perform many <code>:=</code> operations
(e.g. <code>assign_formulas()</code>) may set this to FALSE to avoid attribute-
related shallow-copy warnings.</dd>


<dt>...</dt>
<dd>Reserved for future extensions.</dd>

</dl>

as_peaklist: Check format of peaklist

Description

Usage

Value

Arguments

See Also