issue #27 convert to gwasglue2 summaryset inside gwasvcf package

[ritarasteiro]

• new feature: creating a gwasglue2 SummarySet from a vcf file.
• added new section to guide

NOTE:

• There is an error when creating the vignette, related with the as_tibble function.
• when investigating further, the error was in query_gwas, when proxies = yes. I added name_repair="minimal" to all the calls of as_tibble() in proxy.r without it, but it still is given an error. Need to further investigate.
• @explodecomputer Am I missing something?

ERRORS:

• error when running check()
  ``--- re-building ‘guide.Rmd’ using rmarkdown
  /usr/bin/sqlite3

  Quitting from lines 271-273 [unnamed-chunk-28] (guide.Rmd)
  Error: processing vignette 'guide.Rmd' failed with diagnostics:
  The validate argument of as_tibble() was deprecated in tibble 2.0.0
  and is now defunct.
  ℹ Please use the .name_repair argument instead.
  --- failed re-building ‘guide.Rmd’

  SUMMARY: processing the following file failed:
  ‘guide.Rmd’

  Error: Vignette re-building failed.
  Execution halted
  Error in (function (command = NULL, args = character(), error_on_status = TRUE, …:
  ! System command 'R' failed``

• error when running code in the vignette:
  Error: ! The validateargument ofas_tibble()was deprecated in tibble 2.0.0 and is now defunct. ℹ Please use the.name_repair` argument instead.
  Backtrace:

1. gwasvcf::query_gwas(...)
2. tibble:::as_tibble.data.frame(., .data, .name_repair = "minimal")
3. lifecycle::deprecate_stop(...)
4. lifecycle:::deprecate_stop0(msg)`

[remlapmot]

Additionally on line 73 of R/proxy.R, as with last 2 comments recommend amending

temp <- do.call(rbind, strsplit(ld[["PHASE"]], "")) %>% dplyr::as_tibble(.data, .name_repair="minimal")

to simply

temp <- do.call(rbind, strsplit(ld[["PHASE"]], "")) %>% dplyr::as_tibble(.name_repair="minimal")

[remlapmot]

And the same deletion of .data, is needed on lines 109 and 111 of R/proxy.R as well I think.

[remlapmot]

So I think that's 5 instances of .data, to delete in total.

[remlapmot]

And I recommend adding yourself to the DESCRIPTION as a ctb at least.

[remlapmot]

And I recommend bumping the version number in the DESCRIPTION - we need to get better at remembering to do this in PRs.

[ritarasteiro]

Thanks @remlapmot! I made all the changes and also added a NEWS file.

[remlapmot]

This looks good to me @ritarasteiro .

My last super minor comment is that is usually format the DESCRIPTION by running usethis::use_tidy_description() - which will move gwasglue2 to be in alphabetical order in the Imports list.

Also I think this PR also fixes issue #25. I don't seem to have the rights to add to the Developer pane on this PR page - so I'll put the text below which may hopefully close that issue on merging this.

closes #25

[chenyangsu]

Hi MRCIEU team, Would it be possible to merge these pull requests soon? I'm using your package for a project for finding LD proxies but this error still remains.

Error:
! The validate argument of as_tibble() was deprecated in tibble 2.0.0 and is now defunct.
ℹ Please use the .name_repair argument instead.

In addition, I was able to bypass the error by installing the branch with the new changes:

library(remotes)
install_github("MRCIEU/gwasvcf@27-convert-to-gwasglue2-summaryset-inside-gwasvcf-package")

However, after running
query_gwas(outcome_vcf, rsid=input_rsid, proxies="only", bfile=ld_file, build = "GRCh38", tag_kb = 1000, tag_r2=0.8) there's another error at the align step:

Determining searchspace...
Proxy lookup...
Finding proxies...
Taking input= as a system command ('gunzip -c /tmp/RtmpnitEtI/file3098e72a46191.targets.ld.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Found 24 proxies
Extrating proxies...
Identified proxies for 1 of 1 rsids
Aligning...
Error in all_dims[, 1L] : incorrect number of dimensions

Would it be possible to solve this issue? Thanks a lot!

[remlapmot]

@ritarasteiro / @explodecomputer please merge #31 (if you're happy to) into this branch then merge this into master.

(Note that both of these still don't fix #26 which we'll have to fix after this).

[remlapmot]

This looks good to me now.

[remlapmot]

Thanks for merging #31 @ritarasteiro - note the checks here are just failing because the OpenGWAS server is under heavy load.

Also - it's worth noting I don't have any permissions on this repo - so I can't merge your PRs (even if I approve them - I just checked by approving this one, but I didn't obtain the Merge button). I'd be happy to merge this if you or @explodecomputer want to give me permission in the repo (I could be a backup for Gib when he's busy).

[ritarasteiro]

@remlapmot I just added you with maintainer permissions.

The checks appear to fail when trying to install genetics.binaRies in the guide and in ubuntu. I am also having some problems when trying to install this package locally.

[remlapmot]

@remlapmot I just added you with maintainer permissions.

thanks

The checks appear to fail when trying to install genetics.binaRies in the guide and in ubuntu. I am also having some problems when trying to install this package locally.

Great spot - the genetics.binaRies download fail is because Gib moved that repo from being under his account to under the MRCIEU org. Usually GitHub automatically redirects URLs of moved repos - and if you go to the old repo address it does indeed redirect. However it seems maybe there are some instances where the redirection doesn't occur. So I will send a little fix to genetics.binaRies to use the new-ish MRCIEU address before merging this.

[remlapmot]

@explodecomputer - merging this as it seems good to me.