Manipulate and Explore UK Biobank Data

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Documentation for package ‘ukbtools’ version 0.11.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

ukbtools-package	ukbtools: Manipulate and Explore UK Biobank Data
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
ukbcentre	UKB assessment centre
ukbtools	ukbtools: 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_related_with_data	Subset of the UKB relatedness dataframe with data
ukb_gen_rel_count	Relatedness count
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