MidarExperiment
The MidarExperiment object is the
primary data container in the MiDAR workflow. It holds
all the experimental and processed data and metadata, as well as details
of the applied processing steps and the current status of the data. Most
MiDAR functions take the MidarExperiment
object as data input. Functions that process the data return an updated
MidarExperiment object, which can then be used in
subsequent steps.
Data within the MidarExperiment is organized into data and metadata categories, each
divided into tables (data.frames).
Data
| Category | Table name (Slot) | Description |
|---|---|---|
| Raw Data | dataset_orig |
Original imported analysis data. |
| Processed Data | dataset |
Annotated raw and processed data with available metadata. |
| Feature metrics | feature_metrics |
Information and various quality control metrics for features. |
Metadata
| Data Type | Table name (Slot) | Description |
|---|---|---|
| Analyses Annotation | annot_analyses |
Details sample categories, amounts, dilutions, processing batches, and other relevant information. |
| Features Annotation | annot_features |
Describes internal standards for normalization, response factors, feature classification, and specifies quantifiers and internal standards. |
| Internal Standard | annot_istds |
Concentrations of internal standards added to samples. |
| Batches | annot_batches |
Specifies the boundaries (start and end) for each defined batch. |
| Response Curves | annot_responsecurves |
Defines response curves, detailing sample amounts across different steps. |
| Calibration Curves | annot_standards |
Defines concentrations of unlabelled and labelled standards in calibration curves and other quality control materials. |