Package: ukbnmr 3.2.0
ukbnmr: Removal of Unwanted Technical Variation from UK Biobank NMR Metabolomics Biomarker Data
A suite of utilities for working with the UK Biobank <https://www.ukbiobank.ac.uk/> Nuclear Magnetic Resonance spectroscopy (NMR) metabolomics data <https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=220>. Includes functions for extracting biomarkers from decoded UK Biobank field data, removing unwanted technical variation from biomarker concentrations, computing an extended set of lipid, fatty acid, and cholesterol fractions, and for re-deriving composite biomarkers and ratios after adjusting data for unwanted biological variation. For further details on methods see Ritchie SC et al. Sci Data (2023) <doi:10.1038/s41597-023-01949-y>.
Authors:
ukbnmr_3.2.0.tar.gz
ukbnmr_3.2.0.zip(r-4.5)ukbnmr_3.2.0.zip(r-4.4)ukbnmr_3.2.0.zip(r-4.3)
ukbnmr_3.2.0.tgz(r-4.4-any)ukbnmr_3.2.0.tgz(r-4.3-any)
ukbnmr_3.2.0.tar.gz(r-4.5-noble)ukbnmr_3.2.0.tar.gz(r-4.4-noble)
ukbnmr_3.2.0.tgz(r-4.4-emscripten)ukbnmr_3.2.0.tgz(r-4.3-emscripten)
ukbnmr.pdf |ukbnmr.html✨
ukbnmr/json (API)
NEWS
| # Install 'ukbnmr' in R: |
| install.packages('ukbnmr', repos = c('https://sritchie73.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sritchie73/ukbnmr/issues
- nmr_info - Nightingale biomarker information
- sample_qc_info - Nightingale biomarker sample processing information
- test_data - Data for testing package functions
Last updated 1 days agofrom:d41b5d613f. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 22 2024 |
| R-4.5-win | OK | Nov 22 2024 |
| R-4.5-linux | OK | Nov 22 2024 |
| R-4.4-win | OK | Nov 22 2024 |
| R-4.4-mac | OK | Nov 22 2024 |
| R-4.3-win | OK | Nov 22 2024 |
| R-4.3-mac | OK | Nov 22 2024 |
Exports:compute_extended_ratio_qc_flagscompute_extended_ratiosextract_biomarker_qc_flagsextract_biomarkersextract_sample_qc_flagsrecompute_derived_biomarker_qc_flagsrecompute_derived_biomarkersremove_technical_variation
Dependencies:bitbit64cpp11data.tablegenericslubridateMASStimechange
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Aggregate QC Flags when computing the extended set of biomarker ratios | compute_extended_ratio_qc_flags |
| Compute extended set of biomarker ratios | compute_extended_ratios |
| Extract NMR biomarker QC flags from a data.frame of UK Biobank fields | extract_biomarker_qc_flags |
| Extract NMR metabolomic biomarkers from a data.frame of UK Biobank fields | extract_biomarkers |
| Extract NMR sample QC flags from a data.frame of UK Biobank fields | extract_sample_qc_flags |
| Nightingale biomarker information | nmr_info |
| Aggregate QC Flags when recomputing all composite and derived biomarkers | recompute_derived_biomarker_qc_flags |
| Recompute composite biomarkers and ratios from the 107 non-derived biomarkers | recompute_derived_biomarkers |
| Remove technical variation from NMR biomarker data in UK Biobank. | remove_technical_variation |
| Nightingale biomarker sample processing information | sample_qc_info |
| Data for testing package functions | test_data |
| Tools for processing the UK Biobank NMR metabolomics biomarker data | ukbnmr-package ukbnmr |
