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Problem with obtaining the RAF for individual variants contained within associations with a haplotype #41

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milcs40 opened this issue Jun 2, 2023 · 0 comments
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@milcs40
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milcs40 commented Jun 2, 2023

I have came across a potential issue when using gwasrapidd to get associations with traits, for which multiple SNPs are reported (this is, the association is with an haplotype).

For example, when you run:
get_associations(study_id = "GCST000480"), we pull three associations as reported in the GWAS catalog, but when we inspect the risk_alleles slot, the risk allelic frequency (RAF) (or risk_frequency in gwasrapidd) for the individual SNPs isn't reported.

This means that the RAF that is displayed on the GWAS catalog web interface (which I assume corresponds to the haplotype RAF) is not displayed at all in the gwasrapidd interface.

Despite this small issue, I am loving your tool! Thank you so much!

@ramiromagno ramiromagno self-assigned this Jun 2, 2023
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