The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.
The goal of UKB.COVID19 is to assist with the UK Biobank (UKB) COVID-19 data processing, risk factor association tests and to generate SAIGE GWAS phenotype file.
Note: to access the UKB datasets, you need to register as an UKB researcher. If you are already an approved UKB researcher with a project underway, and wish to receive these datasets for COVID-19 research purposes, you can register to receive these data by logging into the Access Management System (AMS).
You can install the released version of UKB.COVID19 from CRAN with:
OR
OR
This is a basic example which shows you how to creat a covariate file with risk factors using UKBB main tab data: Note: the ukb.tab file must include fields: f.eid, f.31.0.0, f.34.0.0, f.189.0.0, f.21001., f.21000., f.20161.
library(UKB.COVID19)
covar <- risk_factor(ukb.data=covid_example("sim_ukb.tab.gz"),
ABO.data=covid_example("sim_covid19_misc.txt.gz"),
hesin.file=covid_example("sim_hesin.txt.gz"),
res.eng=covid_example("sim_result_england.txt.gz"))This is an example which shows you how to generate a file with COVID-19 susceptibility phenotypes:
susceptibility <- makePhenotypes(ukb.data=covid_example("sim_ukb.tab.gz"),
res.eng=covid_example("sim_result_england.txt.gz"),
death.file=covid_example("sim_death.txt.gz"),
death.cause.file=covid_example("sim_death_cause.txt.gz"),
hesin.file=covid_example("sim_hesin.txt.gz"),
hesin_diag.file=covid_example("sim_hesin_diag.txt.gz"),
hesin_oper.file=covid_example("sim_hesin_oper.txt.gz"),
hesin_critical.file=covid_example("sim_hesin_critical.txt.gz"),
code.file=covid_example("coding240.txt.gz"),
pheno.type = "susceptibility")This is an example which shows you how to generate a file with COVID-19 severity phenotypes:
severity <- makePhenotypes(ukb.data=covid_example("sim_ukb.tab.gz"),
res.eng=covid_example("sim_result_england.txt.gz"),
death.file=covid_example("sim_death.txt.gz"),
death.cause.file=covid_example("sim_death_cause.txt.gz"),
hesin.file=covid_example("sim_hesin.txt.gz"),
hesin_diag.file=covid_example("sim_hesin_diag.txt.gz"),
hesin_oper.file=covid_example("sim_hesin_oper.txt.gz"),
hesin_critical.file=covid_example("sim_hesin_critical.txt.gz"),
code.file=covid_example("coding240.txt.gz"),
pheno.type = "severity")This is an example which shows you how to generate a file with COVID-19 mortality phenotype: Note: the code file is udner /UKB.COVID19/inst/extdata/coding240.txt.gz
mortality <- makePhenotypes(ukb.data=covid_example("sim_ukb.tab.gz"),
res.eng=covid_example("sim_result_england.txt.gz"),
death.file=covid_example("sim_death.txt.gz"),
death.cause.file=covid_example("sim_death_cause.txt.gz"),
hesin.file=covid_example("sim_hesin.txt.gz"),
hesin_diag.file=covid_example("sim_hesin_diag.txt.gz"),
hesin_oper.file=covid_example("sim_hesin_oper.txt.gz"),
hesin_critical.file=covid_example("sim_hesin_critical.txt.gz"),
code.file=covid_example("coding240.txt.gz"),
pheno.type = "mortality")This is an example which shows you how to generate a file with all comorbidities in ICD-10 code and how to perform the association tests between comorbidities and COVID-19: Note: the code file is udner /UKB.COVID19/inst/extdata/ICD10.coding19.txt.gz
# generate comorbidity file
comorb <- comorbidity_summary(ukb.data=covid_example("sim_ukb.tab.gz"),
hesin.file=covid_example("sim_hesin.txt.gz"),
hesin_diag.file=covid_example("sim_hesin_diag.txt.gz"),
ICD10.file=covid_example("ICD10.coding19.txt.gz"),
primary = FALSE,
Date.start = "16/03/2020")
# association tests
comorb.asso <- comorbidity_asso(pheno=susceptibility,
covariates=covar,
cormorbidity=comorb,
population="white",
cov.name=c("sex","age","bmi","SES","smoke","inAgedCare"),
phe.name="pos.neg",
ICD10.file=covid_example("ICD10.coding19.txt.gz"))This is a basic example which shows you how to create sample QC files, and sample inclusion / exclusion lists for specified software:
sampleQC(ukb.data=covid_example("sim_ukb.tab.gz"),
withdrawnFile=covid_example("sim_withdrawn.csv.gz"),
ancestry="all",
software="SAIGE",
outDir=covid_example("results"))This is a basic example which shows you how to create SNP inclusion lists (SNPID and rsID formats) for given MAF/INFO filters. Also outputs list of SNPs to be used for genetic Relatedness Matrix (GRM) calculations.
variantQC(snpQcFile=covid_example("sim_ukb_snp_qc.txt.gz"),
mfiDir=covid_example("alleleFreqs"),
mafFilt=0.001,
infoFilt=0.5,
outDir=covid_example("results"))This is a basic example which shows you how to generate files for GWAS Software. SAIGE and Plink currently supported.
makeGWASFiles(ukb.data=covid_example("sim_ukb.tab.gz"),
pheno=phe,
covariates=covar,
phe.name="hospitalisation",
cov.name=NULL,
includeSampsFile=NULL,
software="SAIGE",
outDir=covid_example("results"),
prefix="hospitalisation")These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.