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Discard unwanted columns #27

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dariushghasemi opened this issue Nov 5, 2024 · 1 comment
Open

Discard unwanted columns #27

dariushghasemi opened this issue Nov 5, 2024 · 1 comment

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@dariushghasemi
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Here we decided to discard the columns created in the conditional pipeline to be used for fine-mapping in the last step of the pipeline. So, we will remove below columns from the conditional or locus breaker results:

  • snp_map: copy of SNP column
  • type: type of phenotype based on measurement
  • sdY: standard deviation of phenotype

Two newly created columns should be removed after that COJO was performed ONLY for formatting sakes:

  • pJ_org: p-value in the joint model from bJ and bJ_se made by GCTA
  • mlog10pJ: minus log10 p-value in the joint model from bJ and bJ_se computed in the conditional pipe
@dariushghasemi
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We also added locus name and extended locus to the COJO and conditional analyses results.

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