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The 1 million sample HAPNEST dataset (https://github.com/pystatgen/sgkit/discussions/1144#discussioncomment-7654640 ) seems ideal for our purposes.
Larger thank ukb, and no messing with data access p…
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I am wondering what's the best strategy to adjust age for UKB-based association analysis? age, diagnosis year? birth year?
Thanks.
Shicheng
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The article I came across that utilized MTAG left me feeling very puzzled about whether I used the MTAG is correct.
1. As per my understanding, if I were to employ MTAG to simultaneously input fo…
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I was trying to QC the 200K UKB WES data using the preprocessing with QC pipeline and I am finding the final genotypes.h5 file to have no genotypes at all (the file size was 8Mb). I did some digging a…
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**Please make sure that this is a bug! If you have questions about how to use TwoSampleMR please use the [Discussions](https://github.com/MRCIEU/TwoSampleMR/discussions) function instead.**
## Desc…
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Dear Joelle,
I am wondering is there any plan to include POLMM (Proportional Odds Logistic Mixed Model) in REGENIE so that categorical outcome could be tested in UKB.
Thanks.
Shicheng
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Sorry, but the snp number in the baselineLD_v2.1_annots download from the Google Cloud can not match the one generated by the user.
ValueError: LD Scores for concatenation must have identical SNP c…
C0nc updated
5 months ago
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I notice you selected a random subset of unrelated samples. two questions:
1) for EUR population, who dataset you used? 1000G_CEU, hapmap_CEU_r23a_filtered, UK10K, HRC reference panel?
2) for EUR…
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Add GWAS catalog file to repo. Add notebook that
- matches diseases from GWAS catalog to our diseases (perhaps use fuzzywuzzy for matching, do some manual matching if needed afterward)
- matches …
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Perform empirical analyses of BMI on a range of disease outcomes in UKB europeans and BBJ
- Perhaps do this in a vignette
- Or do it in mr.trans repository