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).
read_xml_peaklist(folder_path = NULL, ...)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.
(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.
Other internal functions:
create_custom_formula_library(),
extract_aquisition_params(),
extract_aquisition_params_from_folder(),
extract_metadata_from_ufz_files()