S4 Class Representing the MIDAR Dataset

Core class to store raw and processed data, annotations and metadata.

Details

Provides also functions to validate data integrity, to perfom normalization and quantitation based on internal standards and to calculate the QC parameters of the experiment

Slots

analysis_type

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

dataset_orig

Original imported analysis data. Required fields:

dataset

Processed analysis data. Required fields:

dataset_QC_filtered

Processed analysis data. Required fields:

annot_analyses

Annotation of analyses/runs

annot_features

Annotation of measured features.

annot_istd

Annotation of Internal Standard concentrations.

annot_responsecurves

Annotation of Response curves (RQC). Required fields

annot_studysamples

Annotation of study samples. Required fields:

annot_batch_info

Annotation of batches. Required fields:

metrics_qc

QC information 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_drift_corrected

Flag if data has been drift corrected

is_batch_corrected

Flag if data has been batch corrected

is_isotope_corr

Flag if one or more features have been isotope corrected