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VarPhen pipeline - phenotypes #11

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MCorentin opened this issue Nov 26, 2023 · 0 comments
Open

VarPhen pipeline - phenotypes #11

MCorentin opened this issue Nov 26, 2023 · 0 comments
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Due to a change in biomaRt, get_phenotype_terms() does not return a list of phenotypes anymore.

obesity_phens <- get_phenotype_terms(keyword = "obesity", snp_mart = snp_mart)

Error in biomaRt::getBM(attributes = c("chr_name", "chrom_start", "refsnp_id", :
Values argument contains no data.

However, get_variants_from_phenotypes() still works if the user knows the list of phenotypes to use as input.
@MCorentin MCorentin added the bug Something isn't working label Nov 26, 2023
@MCorentin MCorentin self-assigned this Nov 26, 2023
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