47 gwasglue2 output and new ldscores functions

MRCIEU / ieugwasr

R interface to the IEU GWAS database API

https://mrcieu.github.io/ieugwasr/

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47 gwasglue2 output and new ldscores functions #48

Closed ritarasteiro closed 6 months ago

ritarasteiro commented 7 months ago

New features:

associations() outputs a gwasglue2 Summaryset, when gwasglue=TRUE. It uses gwainfo to add the metadata.
new ld_scores.R file:
1. contains a convertor for gwasgue2 variant ID system
2. Reads ieugwasr::afl2_list dataframe and saves ld score compressed files, divided by chr and pop.

ritarasteiro commented 7 months ago

Github actions It appears there is a problem with R versions, when installing gwasglue2 (gwasglue2: Needs R >= 4.0.0; ieugwasr: Needs R>=3.6.

ritarasteiro commented 7 months ago

New feature: tophits() outputs a gwasglue2 Summaryset, when gwasglue=TRUE.
Github action workflow yaml updated
updated R version in DESCRIPTION

ritarasteiro commented 7 months ago

@explodecomputer A few questions:

Should I add the new argument of tophits() and associations() to the vignettes? Or leave it to the gwasglue2 ones?
Do you mind if I add myself as ctb in the author list?
Need to update NEWS

ritarasteiro commented 7 months ago

@remlapmot

Hi Tom, If you have the time ,could you review this PR? Specifically, the updates to the Github actions yaml file. @explodecomputer mention that you created the original one? Note that, there are still a few things to add to the documentation.

Thanks

Rita

remlapmot commented 7 months ago

Happy to review Rita - will probably do tomorrow or Monday.

Great add yourself as ctb or aut; in fact could you add me and Ben Elsworth as well.

remlapmot commented 7 months ago

And at the end of your commits could you rebuild the pkgdown website - literally just need to run pkgdown::build_site() (with R working dir at top level of repo) (as we didn't put a pkgdown GHA workflow in this repo yet, so docs/ dir has to be updated manually, or you could add that workflow from r-lib/actions)

ritarasteiro commented 7 months ago

@remlapmot and @explodecomputer

The usethis::use_github_action("check-full") created a new [R-CMD-check] badge in README.md. Should I maintain the previous [R build status] badge or remove it? My suggestion is to remove it.

ritarasteiro commented 7 months ago

I incremented the package version to v0.1.6.

ritarasteiro commented 7 months ago

Great add yourself as ctb or aut; in fact could you add me and Ben Elsworth as well.

I added the new authors. Do you have a new email for Ben? It appears the one I copied from the DESCRIPTION in TwoSampleMR no longer exist.

ritarasteiro commented 7 months ago

Is there any Issue that needs to be fixed, that can be done in this PR?

ritarasteiro commented 7 months ago

I incremented the package version to v0.1.6.

I was conservative, in incrementing just the patch. However, it probably should be v0.2 as new functionalities were added.

ritarasteiro commented 7 months ago

Thanks @remlapmot. I will make the changes during next week.