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Questions about calculating combined tau-star #32

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Linshiqi-Git opened this issue Apr 8, 2024 · 0 comments
Open

Questions about calculating combined tau-star #32

Linshiqi-Git opened this issue Apr 8, 2024 · 0 comments

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@Linshiqi-Git
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Linshiqi-Git commented Apr 8, 2024

Hi,
I followed the steps outlined in the Readme and utilized the run_ldsc_reg.sh script to compute the disease heritability enrichment signal for each cell type, categorized by annotation type (e.g., based on eQTL or PC Hi-C, etc.). My aim is to combine different annotation types to determine the total disease heritability enrichments for each cell type. To achieve this, I utilized either the ldsc_postprocess_combined_taustar.R or ldsc_postprocess_joint_taustar.R script. However, I am perplexed by the code that the test for tau in the script (meta.summaries) is derived from the results (df) calculated across multiple traits. How does this calculation translate into the disease heritability enrichment of cell types? I would appreciate it if someone could point out where I may be misunderstanding the process.

It's worth mentioning that my resulting directory distribution is:

  • annotation1:
    cell type1:
    trait1.results
    trait1.delete
    trait1.log
    trait1.part_delete
    trait2.results
    trait2.delete
    trait2.log
    trait2.part_delete
    cell type2:
    trait1.results
    trait1.delete
    trait1.log
    trait1.part_delete
    ...
  • annotation2:
    cell type1:
    ...
    cell type2:
    ...
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