extract_sample_qc_flags {ukbnmr} | R Documentation |
Extract NMR sample QC flags 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
sample quality control flags for the NMR metabolomics biomarker data
giving them short variable names.
Usage
extract_sample_qc_flags(x)
Arguments
x |
|
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 sample QC flag, and <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 QC Flag,
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.
Value
a data.frame
or data.table
with column names "eid"
and "visit_index", followed by columns for each sample
QC tag, e.g. "Shipment.Plate", ..., "Low.Protein".
Examples
ukb_data <- ukbnmr::test_data # Toy example dataset for testing package
sample_qc_flags <- extract_sample_qc_flags(ukb_data)