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Improve output report #16

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nebfield opened this issue Feb 23, 2022 · 3 comments
Closed

Improve output report #16

nebfield opened this issue Feb 23, 2022 · 3 comments
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bug Something isn't working enhancement New feature or request

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@nebfield
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nebfield commented Feb 23, 2022

Capture statistics in a consistent way from

  • scorefile_read.py
  • match_variants.py

And add them to the report

Include scorefiles that have been dropped for QC issues

@nebfield nebfield added the enhancement New feature or request label Feb 23, 2022
@smlmbrt
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smlmbrt commented Mar 21, 2022

Variant Matching

  • Summary of selected options (e.g. keep_amb keep_multiallelic)
  • % matched (% of sum of variant weights missing)
  • % ambiguous (if applicable)
  • % fixed-strand flips
  • Current bug: when multiple scores are present it uses the union of variants to calculate the percentages rather than a score-specific %)

Scores

  • Mean, sd, key metadata (pgs_id, trait, publication?)
  • Density plot (and splitting it by ancestry eventually)

@nebfield nebfield changed the title Improve statistics Improve output report May 11, 2022
@smlmbrt smlmbrt added the bug Something isn't working label Jun 30, 2022
@smlmbrt
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smlmbrt commented Sep 16, 2022

Mostly closed in #51

@smlmbrt
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smlmbrt commented Sep 16, 2022

Issue recorded in: PGScatalog/pgscatalog_utils#8

@smlmbrt smlmbrt closed this as completed Sep 16, 2022
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