ukbtools0.11.3 package

Manipulate and Explore UK Biobank Data

ukb_centre

Inserts UKB centre names into data

ukb_context

Demographics of a UKB sample subset

ukb_defunct

Defunct genetic metadata functions

ukb_df

Reads a UK Biobank phenotype fileset and returns a single dataset.

ukb_df_duplicated_name

Checks for duplicated names within a UKB 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_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_read_fam

Reads a PLINK format fam file

ukb_gen_read_sample

Reads an Oxford format sample file

ukb_gen_rel

Creates a table of related individuals

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

ukb_gen_write_plink_excl

Writes a PLINK format file for combined exclusions

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

ukbtools

ukbtools: Manipulate and Explore UK Biobank Data

A set of tools to create a UK Biobank <http://www.ukbiobank.ac.uk/> 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.