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Remove --file-pheno, --col-pheno and --col-pheno-from-fam args in ldpred2.R scripts#142

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ofrei merged 6 commits intomainfrom
fix-124
Mar 8, 2023
Merged

Remove --file-pheno, --col-pheno and --col-pheno-from-fam args in ldpred2.R scripts#142
ofrei merged 6 commits intomainfrom
fix-124

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@espenhgn espenhgn commented Mar 1, 2023 •
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Fixes #124.

Changes proposed in this pull request:

  • Remove --file-pheno, --col-pheno, --col-pheno-from-fam options fromldpred2.R scripts.
  • Remove correlation calculations between PGS and phenotype.

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  • I've updated or added any relevant docstrings following the syntax described in the
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  • If this PR fixes a bug, I've added a test that will fail without my fix.
  • If this PR adds a new feature, I've added tests that sufficiently cover my new functionality.

@espenhgn espenhgn changed the title fix ldpred2.R script if --file-pheno is used fix ldpred2.R script if --file-pheno is used Mar 1, 2023
@espenhgn espenhgn added the bug-fix fixes a bug label Mar 1, 2023
@espenhgn espenhgn marked this pull request as draft March 1, 2023 10:02
@espenhgn espenhgn mentioned this pull request Mar 1, 2023
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@espenhgn espenhgn changed the title fix ldpred2.R script if --file-pheno is used Remove --file-pheno, --col-pheno and --col-pheno-from-fam args for ldpred2.R scripts Mar 6, 2023
@espenhgn espenhgn changed the title Remove --file-pheno, --col-pheno and --col-pheno-from-fam args for ldpred2.R scripts Remove --file-pheno, --col-pheno and --col-pheno-from-fam args in ldpred2.R scripts Mar 6, 2023
@espenhgn espenhgn marked this pull request as ready for review March 6, 2023 15:40
@espenhgn espenhgn requested a review from deepchocolate March 6, 2023 15:40
deepchocolate
deepchocolate approved these changes Mar 7, 2023
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Great, many thanks!

@ofrei ofrei merged commit bf629ce into main Mar 8, 2023
@espenhgn espenhgn deleted the fix-124 branch April 25, 2023 14:35
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LDpred2 issue with MoBa data(?)

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@espenhgn @deepchocolate @ofrei