Manipulate and Explore UK Biobank Data
Inserts UKB centre names into data
Demographics of a UKB sample subset
Defunct genetic metadata functions
Reads a UK Biobank phenotype fileset and returns a single dataset.
Checks for duplicated names within a UKB dataset
Makes a UKB data-field to variable name table for reference or lookup.
Recursively join a list of UKB datasets
Sample exclusions
Inserts NA into phenotype for genetic metadata exclusions
Heterozygosity outliers
Genetic metadata
Genetic principal components
Reads a PLINK format fam file
Reads an Oxford format sample file
Creates a table of related individuals
Relatedness count
Subset of the UKB relatedness dataframe with data
Related samples (with data on the variable of interest) to remove
Sample QC column names
Writes a BGENIE format phenotype or covariate file.
Writes a PLINK format phenotype or covariate file
Writes a PLINK format file for combined exclusions
Retrieves description for a ICD code.
Retrieves diagnoses for an individual.
Frequency of an ICD diagnosis by a target variable
Retrieves diagnoses containing a description.
Returns the prevalence for an ICD diagnosis
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.