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feat: the FineMapper function for one locus #564

Merged
merged 57 commits into from
Apr 5, 2024
Merged

feat: the FineMapper function for one locus #564

merged 57 commits into from
Apr 5, 2024

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addramir
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@addramir addramir commented Apr 2, 2024 •
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✨ Context

This PR adds the function for fine-mapping of one StudyLocus.

🛠 What does this PR implement

StydyLocus, SumaryStatistics and StudyIndex as input.

🙈 Missing

This is the second wrapping functon in the finemapper step. Will be more.

🚦 Before submitting

  • Do these changes cover one single feature (one change at a time)?
  • Did you read the contributor guideline?
  • Did you make sure to update the documentation with your changes?
  • Did you make sure there is no commented out code in this PR?
  • Did you follow conventional commits standards in PR title and commit messages?
  • Did you make sure the branch is up-to-date with the dev branch?
  • Did you write any new necessary tests?
  • Did you make sure the changes pass local tests (make test)?
  • Did you make sure the changes pass pre-commit rules (e.g poetry run pre-commit run --all-files)?

DSuveges and others added 30 commits November 13, 2023 15:19
@DSuveges
test: adding test for pairwiseLD
632ff14
@Daniel-Considine
Merge branch 'dev' into ds_pairwise_ld
e057a8c
@Daniel-Considine
Merge branch 'dev' into ds_pairwise_ld
76cda39
@Daniel-Considine
feat: adding ld matrix extraction
557fade
@Daniel-Considine
Merge branch 'dev' into ds_pairwise_ld
5b96d2e
@Daniel-Considine
chore: merge from dev
c952898
@Daniel-Considine
Merge branch 'dev' into ds_pairwise_ld
70f7a01
@Daniel-Considine
Merge branch 'dev' of https://github.com/opentargets/gentropy into ds…
cbedc3d 
…_pairwise_ld
@Daniel-Considine
Merge branch 'dev' of https://github.com/opentargets/gentropy into ds…
83427d8 
…_pairwise_ld
@Daniel-Considine
Merge branch 'dev' of https://github.com/opentargets/gentropy into ds…
51f66eb 
…_pairwise_ld
@Daniel-Considine
feat: index and block matrix extraction for studyLocus
82107ec
@Daniel-Considine
Merge branch 'dev' of https://github.com/opentargets/gentropy into ds…
4df3dfc 
…_pairwise_ld
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
bce30d2 
for more information, see https://pre-commit.ci
@Daniel-Considine
chore: updating some test files to gentropy
4d09a60
@Daniel-Considine
chore: updating tests
f7dfba1
@Daniel-Considine
chore: updating pairwise_ld_schema for tests
3a629ef
@Daniel-Considine
chore: updating pairwise_ld tests
6ff6b1c
@Daniel-Considine
chore: fix ld_pairwise tests
3fc9cfa
@Daniel-Considine
chore: fix pairwise_ld tests
0d68020
@Daniel-Considine
chore: fix tests
07260a7
@Daniel-Considine
chore: fix tests
65cea4e
@Daniel-Considine
chore: fixing typing for tests
aa19f9f
@Daniel-Considine
chore: fixing tests
e24cac1
@Daniel-Considine
chore: fixing ld tests
4ec36b9
@Daniel-Considine @DSuveges
Update src/gentropy/dataset/study_index.py
0e93adb 
Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com>
@Daniel-Considine
feat: moving functions to their appropriate locations and improving l…
cd4cddf 
…ogic
@Daniel-Considine
Merge branch 'dev' into ds_pairwise_ld
08c63d0
@Daniel-Considine
fix: optimise conversion of BM to NumPy
228c66b
@Daniel-Considine
Merge branch 'dev' into ds_pairwise_ld
b7dea93
@Daniel-Considine
Merge branch 'dev' into ds_pairwise_ld
b666764
@addramir addramir changed the title feat: the FineMapper function for one StudyLocus feat: the FineMapper function for one locus Apr 2, 2024
@addramir addramir marked this pull request as ready for review April 4, 2024 13:42
@addramir addramir merged commit e1d20f3 into dev Apr 5, 2024
4 checks passed
@addramir addramir deleted the ytdc_finemapper_v3 branch April 5, 2024 11:51
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@Daniel-Considine Daniel-Considine Daniel-Considine approved these changes

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@addramir @Daniel-Considine @DSuveges