Package: UKB.COVID19 0.1.6

Longfei Wang

UKB.COVID19: UK Biobank COVID-19 Data Processing and Risk Factor Association Tests

Process UK Biobank COVID-19 test result data for susceptibility, severity and mortality analyses, perform potential non-genetic COVID-19 risk factor and co-morbidity association tests. Wang et al. (2021) <doi:10.5281/zenodo.5174381>.

Authors:Longfei Wang [aut, cre]

UKB.COVID19_0.1.6.tar.gz
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UKB.COVID19.pdf |UKB.COVID19.html✨
UKB.COVID19/json (API)
NEWS

# Install 'UKB.COVID19' in R:

install.packages('UKB.COVID19', repos = c('https://bahlolab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bahlolab/ukb.covid19/issues

On CRAN:

4.00 score 1 stars 4 scripts 285 downloads 10 exports 129 dependencies

Last updated 6 months agofrom:ddd69d471b. Checks:8 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 13 2025
R-4.5-win	OK	Feb 13 2025
R-4.5-mac	OK	Feb 13 2025
R-4.5-linux	OK	Feb 13 2025
R-4.4-win	OK	Feb 13 2025
R-4.4-mac	OK	Feb 13 2025
R-4.3-win	OK	Feb 13 2025
R-4.3-mac	OK	Feb 13 2025

Exports:comorbidity_asso comorbidity_summary covid_example data_reform log_cov makeGWASFiles makePhenotypes risk_factor sampleQC variantQC

Dependencies:askpass backports base64enc bit bit64 blob broom bslib cachem callr cellranger class classInt cli clipr colorspace commonmark conflicted cpp11 crayon curl data.table DBI dbplyr digest dplyr dtplyr e1071 evaluate fansi farver fastmap fontawesome forcats fs gargle generics ggplot2 glue googledrive googlesheets4 gtable haven here highr hms htmltools httpuv httr ids isoband jquerylib jsonlite KernSmooth knitr labeling labelled later lattice lifecycle lubridate magrittr MASS Matrix memoise mgcv mime miniUI modelr munsell nlme openssl pillar pkgconfig prettyunits processx progress promises proxy ps purrr questionr R.cache R.methodsS3 R.oo R.utils R6 ragg rappdirs RColorBrewer Rcpp readr readxl rematch rematch2 reprex rlang rmarkdown rprojroot rstudioapi rvest sass scales selectr shiny sourcetools stringi stringr styler sys systemfonts textshaping tibble tidyr tidyselect tidyverse timechange tinytex tzdb utf8 uuid vctrs viridisLite vroom withr xfun xml2 xtable yaml

Introduction to the UKB.COVID19 Package

Longfei Wang

Rendered fromIntroduction_to_UKB_COVID19.Rmdusingknitr::rmarkdownon Feb 13 2025.

Last update: 2024-08-17
Started: 2024-07-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Generate comorbidity association result file	comorbidity_asso
Create comorbidity summary file	comorbidity_summary
Provide working directory for UKB.COVID19 example files	covid_example
Reform variables	data_reform
Perform association tests between phenotype and covariates	log_cov
Generate files for GWAS Software. SAIGE and Plink currently supported.	makeGWASFiles
Generate COVID-19 phenotypes	makePhenotypes
Generate covariate file	risk_factor
Sample QC for genetic analyses	sampleQC
Variant QC for Genetic Analyses	variantQC