recompute_derived_biomarkers: Recompute composite biomarkers and ratios from the 107...

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

Recompute composite biomarkers and ratios from the 107 non-derived biomarkers

Description

When adjusting biomarkers for unwanted biological covariates, it is desirable to recompute composite biomarkers and ratios to ensure consistency in the adjusted dataset. This function will compute all composite biomarkers and ratios from their parts (see nmr_info for biomarker details).

Usage

recompute_derived_biomarkers(x)

Arguments

x	data.frame containing NMR metabolomics data from UK Biobank. May either be raw field data output by ukbconv or data with column names corresponding to biomarkers listed in nmr_info.

Details

If your UK Biobank project only has access to a subset of biomarkers, then this function will only return the subset of ratios that can be computed from the biomarker data provided.

All biomarkers in the input data are also returned alongside those computed by this function.

Value

a data.frame with all composite biomarkers and ratios (re)computed from the 107 non-derived biomarkers (see nmr_info for details).

See Also

nmr_info for list of computed biomarker ratios, recompute_derived_biomarker_qc_flags() for obtaining an aggregate of the biomarker QC flags from the biomarkers underlying each computed biomarker, and extract_biomarkers() for details on how the raw field data extracted by the Table Exporter tool is processed.

Examples

ukb_data <- ukbnmr::test_data # Toy example dataset for testing package
bio_qc <- recompute_derived_biomarkers(ukb_data)

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