read_xml_peaklist: Read xml peaklists generates ultrahigh-resolution MS analyses

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

Read xml peaklists generates ultrahigh-resolution MS analyses

Description

This function reads multiple FTMS peaklist files in XML format. The function requires the package 'xml2'. that are generated from Bruker FTICRMS and Thermo Orbitrap instruments. A single peaklists containing the file_paths is returned as a data.table A dialog window requests the path to the required directory (recursive = FALSE by default).

Usage

read_xml_peaklist(folder_path = NULL, ...)

Arguments

folder_path	(Optional) The path to the directory containing the XML files. If not provided, the user will be prompted to choose a folder path interactively.
...	Additional arguments passed to methods.

Value

A data.table containing the combined peaklists extracted from all XML files in the selected folder. Each row represents a single peak. The table includes:

• filename – name of the XML file from which the peak originates.

• mz – mass-to-charge ratio of the peak.

• sn – signal-to-noise ratio (if available in the XML).

• res – peak resolution (if available in the XML).

• i_magnitude – peak intensity.

Files that contain no peak entries return a row with filename only. If the package xml2 is not installed, the function returns NULL after printing an informative message.

See Also

Other internal functions: create_custom_formula_library(), extract_aquisition_params(), extract_aquisition_params_from_folder(), extract_metadata_from_ufz_files()

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