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https://github.com/bahlolab/UKB.COVID19
UK Biobank COVID-19 data processing and risk factor association tests
https://github.com/bahlolab/UKB.COVID19
Last synced: 2 days ago
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UK Biobank COVID-19 data processing and risk factor association tests
- Host: GitHub
- URL: https://github.com/bahlolab/UKB.COVID19
- Owner: bahlolab
- License: other
- Created: 2021-02-05T00:04:53.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2022-04-27T05:54:54.000Z (over 2 years ago)
- Last Synced: 2024-04-27T04:42:31.400Z (7 months ago)
- Language: HTML
- Size: 10.9 MB
- Stars: 1
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-uk-biobank - UKB.COVID19 - 19 data processing and risk factor association tests | (Derivation of variables / Electronic health records)
README
# UKB.COVID19
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).
## Installation
You can install the released version of UKB.COVID19 from [CRAN](https://CRAN.R-project.org) with:
``` r
install.packages("UKB.COVID19")
```
OR
```r
install.packages("remotes")
remotes::install_github("bahlolab/UKB.COVID19")
```
OR
```r
install.packages("devtools")
devtools::install_github("bahlolab/UKB.COVID19")
```
## Example
### Risk factor
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.
``` r
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"))
```
### COVID-19 susceptibility
This is an example which shows you how to generate a file with COVID-19 susceptibility phenotypes:
``` r
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")
```
### COVID-19 severity
This is an example which shows you how to generate a file with COVID-19 severity phenotypes:
``` r
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")
```
### COVID-19 mortality
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
``` r
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")
```
### Association tests between COVID-19 and comorbidities
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
``` r
# 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"))
```
### Sample QC
This is a basic example which shows you how to create sample QC files, and sample inclusion / exclusion lists for specified software:
``` r
sampleQC(ukb.data=covid_example("sim_ukb.tab.gz"),
withdrawnFile=covid_example("sim_withdrawn.csv.gz"),
ancestry="all",
software="SAIGE",
outDir=covid_example("results"))
```
### Variant QC
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.
``` r
variantQC(snpQcFile=covid_example("sim_ukb_snp_qc.txt.gz"),
mfiDir=covid_example("alleleFreqs"),
mafFilt=0.001,
infoFilt=0.5,
outDir=covid_example("results"))
```
### Generate GWAS files
This is a basic example which shows you how to generate files for GWAS Software. SAIGE and Plink currently supported.
``` r
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")
```