Function reference • ukbtools

UKB Dataframe Functions to wrangle the UKB data into a dataframe with meaningful column names.
`ukbtools`	ukbtools: Manipulate and Explore UK Biobank Data
`ukb_df()`	Reads a UK Biobank phenotype fileset and returns a single dataset.
`ukb_df_field()`	Makes a UKB data-field to variable name table for reference or lookup.
`ukb_df_full_join()`	Recursively join a list of UKB datasets
`ukb_df_duplicated_name()`	Checks for duplicated names within a UKB dataset
`ukb_centre()`	Inserts UKB centre names into data
`ukb_context()`	Demographics of a UKB sample subset
Genetic Metadata Functions to query the associated genetic sample QC information
`ukb_gen_read_fam()`	Reads a PLINK format fam file
`ukb_gen_read_sample()`	Reads an Oxford format sample file
`ukb_gen_rel_count()`	Relatedness count
`ukb_gen_related_with_data()`	Subset of the UKB relatedness dataframe with data
`ukb_gen_samples_to_remove()`	Related samples (with data on the variable of interest) to remove
`ukb_gen_sqc_names()`	Sample QC column names
`ukb_gen_write_bgenie()`	Writes a BGENIE format phenotype or covariate file.
`ukb_gen_write_plink()`	Writes a PLINK format phenotype or covariate file
Disease Diagnoses Functions to query the UKB hospital episodes statistics.
`ukb_icd_code_meaning()`	Retrieves description for a ICD code.
`ukb_icd_diagnosis()`	Retrieves diagnoses for an individual.
`ukb_icd_freq_by()`	Frequency of an ICD diagnosis by a target variable
`ukb_icd_keyword()`	Retrieves diagnoses containing a description.
`ukb_icd_prevalence()`	Returns the prevalence for an ICD diagnosis
Datasets
`ukbcentre`	UKB assessment centre
`icd10chapters`	International Classification of Diseases Revision 10 (ICD-10) chapters
`icd10codes`	International Classification of Diseases Revision 10 (ICD-10) codes
`icd9chapters`	International Classification of Diseases Revision 9 (ICD-9) chapters
`icd9codes`	International Classification of Diseases Revision 9 (ICD-9) codes
Defunct The genetic metadata functions were written to retrieve genetic metadata from the phenotype file for the interim genotype release. The fields retrieved became obselete when the full genotyping results were released at the end of 2017. With the release of the full sample (500K individuals) genotypes, sample QC (ukb_sqc_v2.txt) and relatedness (ukbA_rel_sP.txt) data are now supplied as separate files. The contents of these files, along with all other genetic files are described in UKB Resource 531.
`ukb_gen_excl()`	Sample exclusions
`ukb_gen_excl_to_na()`	Inserts NA into phenotype for genetic metadata exclusions
`ukb_gen_het()`	Heterozygosity outliers
`ukb_gen_meta()`	Genetic metadata
`ukb_gen_pcs()`	Genetic principal components
`ukb_gen_rel()`	Creates a table of related individuals
`ukb_gen_write_plink_excl()`	Writes a PLINK format file for combined exclusions

Reference

UKB Dataframe

Genetic Metadata

Disease Diagnoses

Datasets

Defunct