S4 class representing the MRMhub dataset

The MRMhubExperiment object is the core data structure utilized within the MRMhub workflow, encapsulating all relevant experimental data and metadata. It also includes processing results, details of the applied processing steps, and the current status of the data.

Slots

title

Title of the experiment

analysis_type

Analysis type, one of "lipidomics", "metabolomics", "externalcalib", "others"

feature_intensity_var

Feature variable used as default for calculations

conc_analyte_unit

Unit of the analyte amount underlying feature_conc, set when the data are quantitated. "pmol" or "ng" for ISTD quantitation (see quantify_by_istd()), or the calibrant concentration unit (e.g. "nmol/L") for calibration quantitation. Divided by sample_amount_unit by get_conc_unit() to name the unit of feature_conc. NA when not quantitated.

dataset_orig

Original imported analysis data. Required fields:

dataset

Processed analysis data. Required fields:

dataset_filtered

Processed analysis data. Required fields:

annot_analyses

Annotation of analyses/runs

annot_features

Annotation of measured features.

annot_istds

Annotation of Internal Standard concs.

annot_responsecurves

Annotation of response curves (RQC). Required fields

annot_qcconcentrations

Annotation of calibration curves. Required fields

annot_studysamples

Annotation of study samples. Required fields:

annot_batches

Annotation of batches. Required fields:

metrics_qc

QC information for each measured feature

metrics_calibration

Calibration metrics calculated from external calibration curves for each measured feature

status_processing

Status within the data processing workflow

is_istd_normalized

Flag if data has been ISTD normalized

is_quantitated

Flag if data has been quantitated using ISTD and sample amount

is_filtered

Flag if data has been filtered based on QC parameters

is_isotope_corr

Flag if one or more features have been isotope corrected

has_outliers_tech

Flag if data has technical analysis/sample outliers

analyses_excluded

Analyses excluded from processing, plots and reporting, unless explicitly requested

features_excluded

Features excluded from processing, plots and reporting, unless explicitly requested

var_drift_corrected

List indicating which variables are drift corrected

var_batch_corrected

List indicating which variables are batch corrected