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We convert the UKB sumstats into LDSC munge format.
This will enable us to perform
- GBE global meta-analysis #25
- Compute LDSC intercept as a GWAS QC metric #21
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Dear Team,
I am wondering whether UKB,FinnGen and GBIM are included or not?
Thanks
SHicheng
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Several imaging derivatives were contributed to the UKB by Mansour et al., 2023. bioRvix, doi: [10.1101/2023.03.10.532036](https://doi.org/10.1101/2023.03.10.532036) and [github.com/sina-mansour/UKB-c…
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I made a comparison between the PLINK2 glm result from the some range versus reading the dosage matrix with seqminer. The result from seqminer is missing some SNPs that appeared in the PLINK result fr…
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Hi,
In step 2 there's usage of a file:
plink2 ... --keep ~/Documents/biobank/ukb_phenotypes/indiv_filtered_v2.txt
However, the closest thing I can see for that file is at step 3 where the fil…
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Hi, I keep encountering errors when conducting clumping. Both TwoSampleMR and ieugwasr packages have been updated. Any insight is appreciated!!
ieugwasr::api_status()
options(ieugwasr_api = 'gwas-…
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- [ ] link to paper/mention COSGAP across main repos.
- [ ] improve usecase using UKB datas
- [x] Add proper citations to original research papers in table with tool overview (fix in documentation)
…
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Hi,
I am trying to run the MAGMA.Celltyping::celltype_associations_pipeline with the following code:
```
MAGMA_results
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Dear Florian
Firstly, I'd like to thank you for developing a robust PRS method, SCT.
I am reproducing the result of 'Making the Most of Clumping and Thresholding for Polygenic Scores'. However, …
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Review of first draft and content improvement