ukbnmr: Tools for processing the UK Biobank NMR metabolomics...

In sritchie73/ukbnmr: Removal of Unwanted Technical Variation from UK Biobank NMR Metabolomics Biomarker Data

Tools for processing the UK Biobank NMR metabolomics biomarker data

Description

@description This package provides utilities for working with the UK Biobank MR metabolomics data. Details are provided below, and in the package vignette (type vignette("ukbnmr") to view).

Details

There are three groups of functions in this package: (1) data extraction, (2) removal of technical variation, and (3) recomputing derived biomarkers and biomarker ratios.

All functions can be applied directly to raw data extracted from UK Biobank.

This package also provides a data.frame of biomarker information, loaded as nmr_info, and data.frame of sample processing information, loaded as sample_qc_info.

Data Extraction Functions

The extract_biomarkers() function will take a phenotype dataset extracted on the UK Biobank Research Analysis Platform by the Table Exporter tool, extract the NMR biomarker fields and give them short comprehensible column names as described in nmr_info. Measurements are also split into multiple rows where a participant has measurements at both baseline and first repeat assessment.

The extract_biomarker_qc_flags() function will take a phenotype dataset extracted on the UK Biobank Research Analysis Platform by the Table Exporter tool, extract the Nightingale quality control flags for each biomarker measurement, returning a single column per biomarker (corresponding to respective columns output by extract_biomarkers()).

The extract_sample_qc_flags() function will take a phenotype dataset extracted on the UK Biobank Research Analysis Platform by the Table Exporter tool and extract the sample quality control tags for the Nightingale NMR metabolomics data.

These functions will also work with older datasets predating the UK Biobank Research Analysis Platform, e.g. those extracted by ukbconv, and/or by the ukbtools R package.

Removal of technical variation

The remove_technical_variation() function will take a phenotype dataset extracted on the UK Biobank Research Analysis Platform by the Table Exporter tool, extract all the biomarkers and QC flags, remove the effects of technical variation on biomarker concentrations, and return a list containing the adjusted NMR biomarker data, biomarker QC flags, and sample quality control and processing information.

This applies a multistep process as described in Ritchie et al. 2023:

1. First biomarker data is filtered to the 107 biomarkers that cannot be derived from any combination of other biomarkers.

2. Absolute concentrations are log transformed, with a small offset applied to biomarkers with concentrations of 0.

3. Each biomarker is adjusted for the time between sample preparation and sample measurement (hours) on a log scale.

4. Each biomarker is adjusted for systematic differences between rows (A-H) on the 96-well shipment plates.

5. Each biomarker is adjusted for remaining systematic differences between columns (1-12) on the 96-well shipment plates.

6. Each biomarker is adjusted for drift over time within each of the six spectrometers. To do so, samples are grouped into 10 bins, within each spectrometer, by the date the majority of samples on their respective 96-well plates were measured.

7. Regression residuals after the sequential adjustments are transformed back to absolute concentrations.

8. Samples belonging to shipment plates that are outliers of non-biological origin are identified and set to missing.

9. The 61 composite biomarkers and 81 biomarker ratios are recomputed from their adjusted parts.

10. An additional 76 biomarker ratios of potential biological significance are computed.

Further details can be found in Ritchie S. C. et al. Quality control and removal of technical variation of NMR metabolic biomarker data in ~120,000 UK Biobank participants, Sci Data 10, 64 (2023). doi: 10.1038/s41597-023-01949-y

Methods for computing biomarker ratios

The compute_extended_ratios() function will compute an extended set of biomarker ratios expanding on the biomarkers available directly from the Nightingale platform. A companion function, compute_extended_ratio_qc_flags(), will aggregate the QC flags for the biomarkers underlying each ratio.

The recompute_derived_biomarkers() function will recompute all composite biomarkers and ratios from 107 non-derived biomarkers, which is useful for ensuring data consistency when adjusting for unwanted biological variation. This includes the extended biomarker rations computed by the compute_extended_ratios() function. A companion function, recompute_derived_biomarker_qc_flags() will aggregate the QC flags for the biomarkers underlying each composite biomarker and ratio.

Author(s)

Maintainer: Scott C Ritchie [e-mail] (0000-0002-8454-9548)

See Also

Useful links:

• Report bugs at https://github.com/sritchie73/ukbnmr/issues

sritchie73/ukbnmr documentation built on Nov. 24, 2024, 8:51 p.m.