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Make complementSumstats.R write file output by default#159

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espenhgn merged 6 commits intomainfrom
fix-157
Apr 25, 2023
Merged

Make complementSumstats.R write file output by default#159
espenhgn merged 6 commits intomainfrom
fix-157

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@espenhgn espenhgn commented Apr 23, 2023

Fixes #157

Changes proposed in this pull request:

  • Made complementSumstats.R script write output to file by default.
  • The default chromosome # output column is CHR (renamed from #CHROM)
  • Added test of rename_column function in fun.R script.

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  • I've updated or added any relevant docstrings following the syntax described in the
    Writing docstrings section of the CONTRIBUTING docs.
  • 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 Up Make complementSumstats.R write file output by default Apr 23, 2023
@espenhgn espenhgn added the enhancement New feature or request label Apr 23, 2023
@espenhgn espenhgn requested a review from deepchocolate April 24, 2023 07:03
@espenhgn espenhgn marked this pull request as draft April 24, 2023 07:33
@espenhgn espenhgn marked this pull request as ready for review April 24, 2023 07:59
@deepchocolate deepchocolate mentioned this pull request Apr 24, 2023
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Great! I've added a fix for one of the test scripts that fails due to `nargs=Inf in #160 .

If you wish, you could add a unittest of rename_columns() in this script:
https://github.com/comorment/containers/blob/f7329b8c38a74194b65d4da23b7e53360e221a5a/usecases/LDpred2_test/unittest/fun.R

But it works as is!

@espenhgn espenhgn merged commit eea44e4 into main Apr 25, 2023
@espenhgn espenhgn deleted the fix-157 branch April 25, 2023 14:31
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LDpred2/complementSumstats.R: rename #CHROM column in output

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