extract_biomarker_qc_flags: Extract NMR biomarker QC flags from a data.frame of UK...

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

Extract NMR biomarker QC flags from a data.frame of UK Biobank fields

Description

Given an input data.frame loaded from a dasaset of NMR metabolomics QC indicator fields extracted by the Table Exporter tool on the UK Biobank Research Analysis Platform, this function extracts the quality control (QC) flags for the NMR metaolomics biomarkers giving them short variable names as listed in the nmr_info information data sheet available in this package. QC Flags are separated by "; " in each column where there are multiple QC Flags for a single measurement.

Usage

extract_biomarker_qc_flags(x)

Arguments

x	data.frame with column names "eid" followed by extracted fields e.g. "p23774_i0_a0", ... "p23774_i1_a0", ..., "p23767_i1".

Details

#' Data sets extracted on the UK Biobank Research Analysis Platform have one row per UK Biobank participant, whose project specific sample identifier is given in the first column named "eid". Columns following this follow a naming scheme based on the unique identifier of each field, assessment visit, and (optionally if relevant) repeated measurement of "p<field_id>_i<visit_index>_a<repeat_index>". For example, the QC flags for the measurement of 3-Hydroxybutyrate at baseline assessment has the column names "p23774_i0_a0", "p23774_i0_a1", and "p23774_i0_a2"; indicating that the 3-Hydroxybutyrate measurement can have up to three QC flags per sample at baseline assessment. Measurements for blood samples collected at the first repeat assessment have 1 in the visit index, e.g. for 3-Hydroxybutyrate at the first repeat assessment there are three columns "p23774_i1_a0", "p23774_i1_a1", "p23774_i1_a2".

The data.frame returned by this function gives each field a unique recognizable name, with measurements from baseline and repeat assessment given in separate rows. The "visit_index" column immediately after the "eid" column indicates whether the biomarker measurement was quantified from the blood samples taken at baseline assessment (visit_index == 0) or first repeat assessment (visit_index == 1). Where multiple QC flags were present at the same measurement, these are collated into a single entry with the multiple QC flags separated by a "; ". Rows are uniquely identifiable by the combination of entries in columns "eid" and "visit_index".

This function will also work with data predating the Research Analysis Platform, including data sets extracted by the ukbconv tool and/or 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
biomarker_qc_flags <- extract_biomarker_qc_flags(ukb_data)

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