extract_biomarkers {ukbnmr}

Extract NMR metabolomic biomarkers from a data.frame of UK Biobank fields

Description

Given an input data.frame loaded from a dataset extracted by ukbconv extracts the UK Biobank fields corresponding to the NMR metabolomics biomarkers giving them short variable names as listed in the nmr_info information data sheet available in this package.

Usage

extract_biomarkers(x)

Arguments

x

data.frame with column names "eid" followed by extracted fields e.g. "23474-0.0", "23474-1.0", ..., "23467-1.0".

Details

Data sets extracted by ukbconv have one row per UKB biobank participant whose project specific sample identifier is given in the first column named "eid". Columns following this have the format "<field_id>-<visit_index>.<repeat_index>", where here <field_id> corresponds to a biomarker of interest, e.g. 23474 for 3-Hydroxybutyrate, <visit_index> corresponds to the assessment time point, e.g. 0 for baseline assessment, 1 for first repeat visit. For the UKB NMR data, the <repeat_index> column is reserved for cases where biomarker measurements have more than one QC Flag (see extract_biomarker_qc_flags()).

In the returned data.frame there is single column for each biomarker, with an additional column for the visit index. Rows are uniquely identifiable by the combination of entries in columns "eid" and "visit_index". There are currently no repeat measure data for the NMR biomarker data in UKB, so no repeat_index column is returned.

This function will also work with data extracted by the ukbtools R package.

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.

A data.table will be returned instead of a data.frame if the the user has loaded the package into their R session.

Value

a data.frame or data.table with column names "eid", and "visit_index", followed by columns for each biomarker e.g. "bOHbutyrate", ..., "Valine".

Examples

ukb_data <- ukbnmr::test_data # Toy example dataset for testing package
nmr <- extract_biomarkers(ukb_data)