ukbtools: Manipulate and Explore UK Biobank Data

A set of tools to create a UK Biobank dataset from a UKB fileset (.tab, .r, .html), visualize primary demographic data for a sample subset, query ICD diagnoses, retrieve genetic metadata, read and write standard file formats for genetic analyses.

UKB Dataframe

Functions to wrangle the UKB data into a dataframe with meaningful column names.

• ukb_df

• ukb_df_field

• ukb_df_full_join

• ukb_df_duplicated_name

• ukb_centre

• ukb_context

Genetic Metadata

Functions to query the associated genetic sample QC information.

• ukb_gen_read_fam

• ukb_gen_read_sample

• ukb_gen_rel_count

• ukb_gen_related_with_data

• ukb_gen_samples_to_remove

• ukb_gen_sqc_names

• ukb_gen_write_bgenie

• ukb_gen_write_plink

Disease Diagnoses

Functions to query the UKB hospital episodes statistics.

• ukb_icd_code_meaning

• ukb_icd_diagnosis

• ukb_icd_freq_by

• ukb_icd_keyword

• ukb_icd_prevalence

Datasets

• ukbcentre

• icd10chapters

• icd10codes

• icd9chapters

• icd9codes