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Updating summary stats schema and ingtesion #266

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merged 2 commits into from
Nov 21, 2023
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DSuveges
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Details under this ticket: 3039

  • Removing upper and lower confidence interval of beta
  • Adding support for variant wise sample size.
  • Sample size parsed from GWAS Catalog summary stats.
  • Sample size added to study locus (collected field after the window based clumping)
  • Sample summary stats dataset updated (columns removed)
  • Sumstats mock logic updated.
  • New filter applied: dropping associations with beta = 0
  • Ingestion updated for GWAS, Finngen.

There are a handful of logic defined under the the above mentioned ticket, that I haven't addressed yet. I feel they have marginal importance in terms of scale:

 For the rest of snps if se==0 and p-value!=1 and p-value!=0 -> infer se from p-value and beta, otherwise drop
 For the rest of snps if p-value==1 or p-value==0 - infer it form beta and se
 If p-value is too small (0) even after inferring -> replace zero with 2e-308

@DSuveges DSuveges requested a review from d0choa November 21, 2023 10:20
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Codecov Report

Merging #266 (0acb106) into main (4997432) will increase coverage by 0.00%.
The diff coverage is 100.00%.

Additional details and impacted files

Impacted file tree graph

@@           Coverage Diff           @@
##             main     #266   +/-   ##
=======================================
  Coverage   86.64%   86.65%           
=======================================
  Files          81       81           
  Lines        1857     1858    +1     
=======================================
+ Hits         1609     1610    +1     
  Misses        248      248           
Files Coverage Δ
src/otg/datasource/finngen/summary_stats.py 100.00% <100.00%> (ø)
.../otg/datasource/gwas_catalog/summary_statistics.py 100.00% <100.00%> (ø)

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hopefully we won't change this in a long time :)

@d0choa d0choa merged commit 09dd2bc into main Nov 21, 2023
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@d0choa d0choa deleted the ds_3039_sumstats_update branch November 21, 2023 11:51
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3 participants