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I’m currently working on imputation for a merged cohort, but I’ve encountered repeated failures specifically with chromosome 9, and the cause isn’t clear. I’ve attached a text file with the relevant s…
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Hi there!
Thank you for the practical package. I have a question regarding the coloc.abf function when running it between my eQTL and GWAS data, both derived from the same samples. Here’s the code …
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Hi there,
When I try to compute Fst using GEAR, I found there is no RAF_SE columns in my GWAS summary statistics and in 1KG reference panel frq.file.
How can I get RAF_SE columns? Should I sample t…
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Hi dougspeed,
Thanks for the hard work to develop this excellent genetic tool. I successfully run the procedure in my data but here I got a problem during the result interpretation after calculatin…
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Hello!
it would be great if a tutorial could be created for performing cell type specific analysis, where analysis uses as input a) your own single-cell data b) downloaded GWAS summary statistics.
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datasets /var/folders/l9/bl9qs09j6nn7q514r12f2z140000gn/T//RtmpXqi45h/ebi-a-GCST90027158.vcf.gz
Downloading with download.file.
trying URL 'https://gwas.mrcieu.ac.uk/files/ebi-a-GCST90027158/ebi-a-…
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Hi,
I am using your tool to calculate my own summary data from UKB. Because my raw data is the imputed genotype data, i used the UKB_imputed_SVD_eigen99_extraction as panel.
I have calculate about …
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# Association
- [ ] [A simple, consistent estimator of heritability for genome-wide association studies]( https://www.biorxiv.org/content/biorxiv/early/2017/10/17/204446.full.pdf)
- [x] [Multivari…
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I want to run rg with two GWAS summary statistics, both derived from Finngen. Should I make some additional restrictions to correct sample overlap?
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As our work on this package progress, this issue can help us enumerate possible future features of the package depending on the time and interests of contributors. Some features will be needed for th…