diff --git a/DESCRIPTION b/DESCRIPTION index c00abb3..5782435 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: MungeSumstats Type: Package Title: Standardise summary statistics from GWAS -Version: 1.15.11 +Version: 1.15.12 Authors@R: c(person(given = "Alan", family = "Murphy", diff --git a/README.md b/README.md index 9988d28..8720f58 100644 --- a/README.md +++ b/README.md @@ -4,16 +4,16 @@ Authors: Alan Murphy, Brian Schilder and Nathan Skene
-Updated: Oct-30-2024 +Updated: Dec-18-2024
[![](https://img.shields.io/badge/release%20version-1.10.1-black.svg)](https://www.bioconductor.org/packages/MungeSumstats) -[![](https://img.shields.io/badge/devel%20version-1.15.1-black.svg)](https://github.com/neurogenomics/MungeSumstats) +[![](https://img.shields.io/badge/devel%20version-1.15.12-black.svg)](https://github.com/neurogenomics/MungeSumstats) [![](https://img.shields.io/github/last-commit/neurogenomics/MungeSumstats.svg)](https://github.com/neurogenomics/MungeSumstats/commits/master) -[![](https://img.shields.io/badge/download-21632/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/MungeSumstats) +[![](https://img.shields.io/badge/download-22669/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/MungeSumstats) [![License: Artistic-2.0](https://img.shields.io/badge/license-Artistic--2.0-blue.svg)](https://cran.r-project.org/web/licenses/Artistic-2.0) [![](https://img.shields.io/badge/doi-https://doi.org/10.1093/bioinformatics/btab665-blue.svg)](https://doi.org/https://doi.org/10.1093/bioinformatics/btab665) @@ -111,6 +111,26 @@ for information on how to use MungeSumstats to access, standardise and perform quality control on GWAS Summary Statistics from the MRC IEU [Open GWAS Project](https://gwas.mrcieu.ac.uk/). +**NOTE** to authenticate, you need to generate a token from the OpenGWAS +website. The token behaves like a password, and it will be used to +authorise the requests you make to the OpenGWAS API. Here are the steps +to generate the token and then have `ieugwasr` automatically use it for +your queries: + +1. Login to +2. Generate a new token +3. Add `OPENGWAS_JWT=` to your .Renviron file, thi can be edited + in R by running `usethis::edit_r_environ()` +4. Restart your R session +5. To check that your token is being recognised, run + `ieugwasr::get_opengwas_jwt()`. If it returns a long random string + then you are authenticated. +6. To check that your token is working, run `ieugwasr::user()`. It will + make a request to the API for your user information using your + token. It should return a list with your user information. If it + returns an error, then your token is not working. +7. Make sure you have submitted use + Please read carefully through the [FAQ website](https://github.com/Al-Murphy/MungeSumstats/wiki/FAQ) for an queries about running MungeSumstats. If you have any outside of this