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Export an experiment to mzTab-M (HUPO-PSI)

Source: R/data-mztab.R
save_dataset_mztab.Rd

Writes an MRMhubExperiment to an mzTab-M 2.0.0-M file, the HUPO-PSI community standard for reporting quantitative metabolomics / lipidomics results (and the format expected by repositories such as MetaboLights).

Usage

save_dataset_mztab(
  data = NULL,
  path,
  variable = "conc",
  instrument = NULL,
  contact = NULL,
  publication = NULL,
  rt_in_minutes = TRUE,
  overwrite = TRUE
)

Arguments

data

An MRMhubExperiment object.

path

Output file path. A .mzTab extension is appended if missing.

variable

Feature variable used as abundance. One of "conc", "intensity", "norm_intensity", "area" or "height". Default "conc" (falls back to "intensity" if not quantified).

instrument, contact, publication

Optional single strings used to enrich the MTD metadata header (instrument name, contact name, publication identifier). NULL (default) omits them.

rt_in_minutes

Logical; are feature_rt values in minutes? mzTab-M stores retention time in seconds, so values are multiplied by 60 when TRUE (default).

overwrite

Logical; overwrite an existing file. Default TRUE.

Value

Invisibly returns the (normalised) output path. Called for its side effect of writing the file.

Details

The full dataset is exported: every analysis becomes an assay (QC, blank and calibration samples included), every feature a Small Molecule Feature (SMF) row, and features are grouped by analyte into Small Molecule Summary (SML) rows. A minimal Small Molecule Evidence (SME) row is emitted per feature so all three table types are present.

Abundance. variable selects which feature_* value is written to the abundance_assay[n] columns. The default "conc" uses final concentrations and declares the matching concentration unit; if the experiment has not been quantified, the exporter falls back to raw feature_intensity with an "Arbitrary quantification unit".

What is not exported. mzTab-M is a quantification report, not a processing-state container. Internal-standard relationships, QC/calibration metrics, drift/batch-correction state and the qc_type/batch structure are not representable and are therefore not written (ISTD features are merely flagged via an opt_global_is_internal_standard column). See the mzTab-M export recipe article for the full mapping.

See also

save_report_xlsx(), save_dataset_csv()

Examples

if (FALSE) { # \dontrun{
save_dataset_mztab(mexp, "experiment.mzTab")
save_dataset_mztab(mexp, "raw.mzTab", variable = "area")
} # }