projectglow / glow

An open-source toolkit for large-scale genomic analysis

https://projectglow.io

Apache License 2.0

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Update GloWGR documentation to fully reflect GloWGR API changes #365

Closed kianfar77 closed 2 years ago

kianfar77 commented 3 years ago

Signed-off-by: kianfar77 kiavash.kianfar@databricks.com

What changes are proposed in this pull request?

(Details)

How is this patch tested?

[ ] Unit tests
[ ] Integration tests
[ ] Manual tests

(Details)

codecov[bot] commented 3 years ago

Codecov Report

Merging #365 (8acd92b) into master (2bf0360) will not change coverage. The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master     #365   +/-   ##
=======================================
  Coverage   93.69%   93.69%           
=======================================
  Files          95       95           
  Lines        4823     4823           
  Branches      473      473           
=======================================
  Hits         4519     4519           
  Misses        304      304

Impacted Files	Coverage Δ
core/src/main/scala/io/projectglow/Glow.scala	`95.65% <100.00%> (ø)`

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ConnorBarnhill commented 3 years ago

Also, I think it would be helpful to add documentation to the GWAS methods explicitly stating that the phenotype and covariate dataframe indices need to be in the same order as the values array of the variant data. Or add an input to the methods that takes the ordered sample IDs returned by glow.wgr.get_sample_ids and handle the re-ordering in the method

williambrandler commented 3 years ago

@kianfar77 please address comments from @karenfeng and we'll merge this in, thanks

kianfar77 commented 3 years ago

@williambrandler This needs much more work. The documentation on website is out of date after we I simplified APIs and made changes to WGR to match Regenie. I was in the middle of documenting stuff and this PR is a WIP. Never got the chance to work on it more.

williambrandler commented 3 years ago

OK, set a meeting on monday

@williambrandler This needs much more work. The documentation on website is out of date after we I simplified APIs and made changes to WGR to match Regenie. I was in the middle of documenting stuff and this PR is a WIP. Never got the chance to work on it more.