export_ume_results: Export UME Analysis Results

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

Export UME Analysis Results

Description

Exports UME analysis results to a structured output folder. The function writes the following objects to CSV (if provided):

• pl – peaklist

• mfd – full molecular formula dataset

• mfd_filt – filtered MFD

• mfd_filt_tf – transformed filtered MFD

• mfd_filt_tf_pivot – pivoted intensity matrix

• ds_tf – transformed diagnostics / statistics

Optionally, the function can export plot objects, create a ZIP archive of all exported files, and write a metadata file (metadata.R) containing a reproducibility snapshot that can be used later in load_ume_results().

Usage

export_ume_results(
  pl,
  mfd,
  mfd_filt = NULL,
  mfd_filt_tf = NULL,
  mfd_filt_tf_pivot = NULL,
  ds_tf = NULL,
  outdir = NULL,
  prefix = "ume",
  figures = FALSE,
  fig_width = 8,
  fig_height = 6,
  fig_device = c("png", "pdf"),
  zip = TRUE,
  metadata = list(),
  env = parent.frame()
)

Arguments

pl	data.table containing peak data. Mandatory columns include neutral molecular mass (mass), peak magnitude (i_magnitude), and a peak identifier (peak_id).
mfd	data.table with molecular formula data as derived from ume::assign_formulas. Column names of elements/isotopes must match names in the isotope column of ume::masses; values are integers representing counts per formula.
mfd_filt	data.table or coercible object. Filtered version of the molecular formula dataset (optional).
mfd_filt_tf	data.table or coercible object. Transformed filtered MFD used in downstream calculations (optional).
mfd_filt_tf_pivot	data.table or coercible object. Pivoted / wide-format intensity matrix derived from mfd_filt_tf (optional).
ds_tf	data.table or coercible object. Transformed diagnostic statistics (optional).
outdir	Character. Output directory in which all export files are stored. The directory is created if it does not exist. Must be provided explicitly; no default is used to comply with CRAN policies on writing to the user's filespace. For temporary exports, use e.g. outdir = file.path(tempdir(), "ume_export").
prefix	Character. Prefix for all exported file names (e.g., "SRFA_001"). Default: "ume".
figures	Controls figure export: FALSE – no figures are exported TRUE – export all plot-like objects found in env character vector – export only the listed object names Recognized plot types are: ggplot, plotly, and recordedplot (base R).
fig_width, fig_height	Numeric. Dimensions of exported figures in inches. Default: 8 × 6.
fig_device	Character. File format for figure export. One of "png" (default) or "pdf".
zip	Logical. If TRUE (default), the exported directory is compressed into a .zip file in the same parent directory as outdir.
metadata	Named list. Additional metadata to write into metadata.R (e.g., analysis settings, instrument parameters, user comments). Default: empty list.
env	Environment. Environment from which figure objects should be collected. Default: parent.frame().

Details

Export UME Analysis Results

Value

Invisibly returns:

• the path to the ZIP file (if zip = TRUE), or

• the path to the output directory (if zip = FALSE).

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