Package: ukbtools 0.11.3.9000

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.

Authors:Ken Hanscombe [aut, cre]

ukbtools_0.11.3.9000.tar.gz
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ukbtools_0.11.3.9000.tgz(r-4.4-any)ukbtools_0.11.3.9000.tgz(r-4.3-any)
ukbtools_0.11.3.9000.tar.gz(r-4.5-noble)ukbtools_0.11.3.9000.tar.gz(r-4.4-noble)
ukbtools_0.11.3.9000.tgz(r-4.4-emscripten)ukbtools_0.11.3.9000.tgz(r-4.3-emscripten)
ukbtools.pdf |ukbtools.html✨
ukbtools/json (API)
NEWS

# Install 'ukbtools' in R:
install.packages('ukbtools', repos = c('https://kenhanscombe.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/kenhanscombe/ukbtools/issues

Datasets:
  • 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

On CRAN:

biobankkcl-sguuk-biobankukb

6.75 score 96 stars 117 scripts 323 downloads 1 mentions 26 exports 61 dependencies

Last updated 2 years agofrom:d0e3248eae. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 15 2024
R-4.5-winNOTENov 15 2024
R-4.5-linuxNOTENov 15 2024
R-4.4-winNOTENov 15 2024
R-4.4-macNOTENov 15 2024
R-4.3-winNOTENov 15 2024
R-4.3-macNOTENov 15 2024

Exports:ukb_centreukb_contextukb_dfukb_df_duplicated_nameukb_df_fieldukb_df_full_joinukb_gen_exclukb_gen_excl_to_naukb_gen_hetukb_gen_metaukb_gen_pcsukb_gen_read_famukb_gen_read_sampleukb_gen_relukb_gen_rel_countukb_gen_related_with_dataukb_gen_samples_to_removeukb_gen_sqc_namesukb_gen_write_bgenieukb_gen_write_plinkukb_gen_write_plink_exclukb_icd_code_meaningukb_icd_diagnosisukb_icd_freq_byukb_icd_keywordukb_icd_prevalence

Dependencies:askpassbitbit64clicliprcodetoolscolorspacecpp11crayoncurldata.tabledoParalleldplyrfansifarverforeachgenericsggplot2gluegtablehmshttrisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerreadrrlangrvestscalesselectrstringistringrsystibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrxml2

Explore UK Biobank data

Ken B. Hanscombe

Rendered fromexplore-ukb-data.Rmdusingknitr::rmarkdownon Nov 15 2024.

Last update: 2019-05-15
Started: 2017-02-17

Readme and manuals

Help Manual

Help pageTopics
International Classification of Diseases Revision 10 (ICD-10) chaptersicd10chapters
International Classification of Diseases Revision 10 (ICD-10) codesicd10codes
International Classification of Diseases Revision 9 (ICD-9) chaptersicd9chapters
International Classification of Diseases Revision 9 (ICD-9) codesicd9codes
Inserts UKB centre names into dataukb_centre
Demographics of a UKB sample subsetukb_context
Reads a UK Biobank phenotype fileset and returns a single dataset.ukb_df
Checks for duplicated names within a UKB datasetukb_df_duplicated_name
Makes a UKB data-field to variable name table for reference or lookup.ukb_df_field
Recursively join a list of UKB datasetsukb_df_full_join
Sample exclusionsukb_gen_excl
Inserts NA into phenotype for genetic metadata exclusionsukb_gen_excl_to_na
Heterozygosity outliersukb_gen_het
Genetic metadataukb_gen_meta
Genetic principal componentsukb_gen_pcs
Reads a PLINK format fam fileukb_gen_read_fam
Reads an Oxford format sample fileukb_gen_read_sample
Creates a table of related individualsukb_gen_rel
Relatedness countukb_gen_rel_count
Subset of the UKB relatedness dataframe with dataukb_gen_related_with_data
Related samples (with data on the variable of interest) to removeukb_gen_samples_to_remove
Sample QC column namesukb_gen_sqc_names
Writes a BGENIE format phenotype or covariate file.ukb_gen_write_bgenie
Writes a PLINK format phenotype or covariate fileukb_gen_write_plink
Writes a PLINK format file for combined exclusionsukb_gen_write_plink_excl
Retrieves description for a ICD code.ukb_icd_code_meaning
Retrieves diagnoses for an individual.ukb_icd_diagnosis
Frequency of an ICD diagnosis by a target variableukb_icd_freq_by
Retrieves diagnoses containing a description.ukb_icd_keyword
Returns the prevalence for an ICD diagnosisukb_icd_prevalence
UKB assessment centreukbcentre
ukbtools: Manipulate and Explore UK Biobank Dataukbtools